At first glance the frozen bundles could be mistaken for conventional joints of meat. But as Ib Pedersen, a Danish pig farmer, lifts them carefully out of the freezer it becomes apparent they are in fact whole piglets - some horribly deformed, with growths or other abnormalities, others stunted.

Inside the farmhouse, piles of paperwork are laid out across a vast table; print outs, reports, statistics, scientific research, correspondence. Pedersen shows me photos - there's more piglets with spinal deformities, their back legs dragging on the ground; others have visible problems with their faces, limbs or tails. There's even a siamese twin - two animals joined at the head.

Pedersen believes these abnormalities were caused - at least in part - by the presence of the herbicide glyphosate in his pig feed. Glyphosate is routinely sprayed on many Genetically Modified (GM) soya and cereal crops to kill weeds and maximise yields, or used as a desiccant in non-GM soya and other grains used in animal feed. Traces of glyphosate can be found in both GM and non-GM animal feed ingredients.

The farmer, who produces 13,000 pigs a year and supplies Europe's largest pork company Danish Crown, says he became so alarmed at the apparent levels of deformity, sickness, deaths, and poor productivity he was witnessing in his animals that he decided to experiment with a different feed: he changed their diet from a GM to a non-GM feed.

Despite not all of the apparent problems disappearing, the results, he says, were still remarkable: "When using GM feed I saw symptoms of bloat, stomach ulcers, high rates of diarrhoea... but when I switched [to non GM feed] these problems went away, some within a matter of days."

The farmer says that not only has the switch in diet improved the visible health of the pigs, it has made the farm more profitable, with less medicine use and higher productivity. "Less abortions, more piglets born in each litter, and breeding animals living longer." He also maintains that man hours have been reduced, with less cleaning needed and fewer complications with the animals.

Although glyphosate is used on conventional crops, its usage on GM soya and maize is particularly prevalent as the crops are engineered to be resistant to the chemical, killing the weeds but leaving the crop plants unaffected.

The introduction of GM crops resistant to glyphosate allowed crops to be sprayed with the herbicide to control weeds - often many times over a growing season - without killing the crop. But this also led to much higher levels of glyphosate in the plants and seeds.

After glyphosate-resistant strains of soy were introduced in 1996, EU regulators raised the allowed maximum residue limit (MRL) for glyphosate in imported soy 200-fold, from 0.1 mg/kg to 20 mg/kg.

Glyphosate use has become increasingly controversial in recent years, with a growing body of research, say campaigners, suggesting that exposure, even at low levels, can be harmful to animals and humans.

Studies have also suggested, claim critics, that the herbicide may disrupt the human endocrine system, which regulates the body's biological processes, meaning that any level of exposure could pose a significant risk to health.

Such claims are vigorously refuted by the agro-chemical industry, who state the herbicide is safe and who accuse campaigners of touting flawed research, or manipulating the findings to suit their own agenda.

Pedersen claims that independent testing revealed all of his deformed pigs had glyphosate in their organs. He shows me a chart he suggests shows a clear correlation between the volume of glyphosate found in pig feed and higher numbers of cranial and spinal deformities. "The more glyphosate, the more deformities," he says, bluntly.

Outside, along a muddy track through a number of arable fields - in addition to pigs, Pedersen produces strawberries, peas and potatoes - we come to the main pig house. It's vast and crowded, efficient and noisy, with the unmistakable stink of pig waste. A factory farm.

Pedersen shows me the farrowing crates, the large bodies of the nursing sows squeezed under metal bars, surrounded by up to a dozen weaning piglets. He points out his best animals - the most productive, the veterans - and stops to check on those he has concerns about, examining a swollen joint here or an inflamed nipple there. Antibiotics are administered to one.

In the main hall the pigs move more freely, as they do in a series of smaller rooms where younger animals are kept as they grow. The farmer manually throws down handfuls of sandy-looking feed to supplement that available in the conical feed troughs. The feed mix, he explains, contains soya, fishmeal and other ingredients - but nothing of GM origin.

Pederson admits his work isn't scientific but says the results should alarm people. He's worried that many farmers have no idea of the potential impact of using feed containing glyphosate, or using GM feed, and that the same is true for consumers: “when using GM feed, he says, "Everything was down in the quagmire ... We had eleven pigs die in one day."

Dormities and deaths "the new normal"

The farmer's research, and outspoken stance, provoked a storm of controversy in Danish agricultural circles after the respected farming publication Effektivt Landbrug featured the story, interviewing Pedersen in detail and referring to the pig farmers' suggestion that DDT and thalidomide - linked to deformities in up to 10,000 babies - could be regarded as trivial compared to the potential risks from GM and glyphosate.

Critics accused him of scaremongering and slammed the findings as unscientific and "without merit" - pointing out that if the claims were true, thousands of other farmers using GM feed would be recording similar problems.

Despite this, Pedersen's work has prompted the Danish Pig Research Centre (VSP) to announce an in-depth study to test the effects of GM and non-GM soya on animal health. The findings of the research have yet to be published.

And Pedersen's findings are beginning to spread well beyond Denmark; earlier this month the German television channel ARD broadcast a documentary featuring the farmer's claims, and Pedersen himself recently travelled to the UK to address a packed symposium at the House of Commons, organised by the All-Party Parliamentary Group On Agroecology.

Anti-GM campaigners say the findings are particularly compelling as the observations were made in a real farm setting, not a laboratory. Claire Robinson of GM Watch told The Ecologist.

"The findings are worrying and consistent with reports from some farmers and vets in the US, who noticed a downturn in the health and reproductive performance in pigs and cattle after GM feed became common."

"Farmers who have worked to exclude GM ingredients from their feed report dramatic improvements in herd health. Farmers should be worried and should not settle for what some scientists are calling a 'new norm' of increased rates of malformations, deaths and digestive and reproductive problems, as GM feed becomes more common."

Peter Melchett, of the Soil Association, says: "Farmers in countries as far apart as Denmark and India have been saying for many years that they have noticed serious ill-health in their animals when feeding GM feed ... practical research on pigs has shown significant impact of GM compared to non-GM feed."

The Danish farmer's claims have also been supported by veterinary experts. Professor Monika Kruger, of Leipzig University, says there is growing evidence showing that glyphosate is dangerous for both animals and people:

"A lot of livestock are ill and nobody is interested. In most cases the highest concentrations come from GM products like soya, rapeseed and corn. We [have] also found glyphosate in meat."

Professor Kruger, who's own research suggested that glyphosate may be toxic to dairy cows, and apparently linked to cases of botulism in cattle, says farmers - and the wider food industry including supermarkets - should be "very concerned" about the claims, and believes that glyphosate should be "eliminated" from farming.

Her comments follow the publication last year of controversial research by Professor Gilles-Eric Seralini, an expert in molecular biology at Caen University in France, which claimed that rats fed a diet of GM maize, or exposed to glyphosate, for two years, developed higher levels of cancers and died earlier than controls.

The study, published in the peer reviewed publication Food and Chemical Toxicology, was the first of its kind to test the impact of GM, and glyphosate, over such a long period - many previous experiments lasted 90 days. The findings led Seralini to argue that glyphosate's apparent endocrine disrupting effects might be responsible.

The study was criticised by the agribusiness industry and academics however, who said it contained methodological flaws, was scientifically substandard, and its findings sensationalised.

A review by the European Food Safety Authority later concluded that Seralini's research could not be regarded as scientifically sound because of inadequacies in the design, reporting and analysis of the study. This has been challenged by the research team.

More recently, research led by Dr. Judy Carman, Associate Professor at Flinders University, Adelaide, claimed that pig health could be harmed by the consumption of feed containing GM crops.

Carmen studied two sets of pigs - one fed a GM diet, one a non-GM diet - from a US piggery over a period of more than five months. Each group was farmed identically in terms of housing and feeding conditions, before being slaughtered and autopsied.

The researchers found that the GM-fed females had, on average, a 25 per cent heavier uterus than non-GM-fed females, 'a possible indicator of disease' according to the study team. The level of severe inflammation in stomachs was also reportedly higher in pigs fed on the GM diet.

Howard Vlieger, an Iowa-based farmer and one of the co-ordinators of Carman's study, told The Ecologist:

"There is little doubt based on the results of putting GM feed into a livestock ration and based on results of removing GM feed from a ration that animal health is better on conventional feed and grain."

Vlieger, when launching the study, said: "In my experience, farmers have found increased production costs and escalating antibiotic use when feeding GM crops. In some operations, the livestock death loss is high, and there are unexplained problems including spontaneous abortions, deformities of new-born animals, and an overall listlessness and lack of contentment in the animals."

As with Seralini's study, Carmen's work was criticised by some academics who accused the researchers of picking out a few "statistically significant" results from a large number of tests, and for using poor statistical methodology for assessing differences in inflammation.

GM "being forced onto farmers"

About 30 million tonnes of GM animal feed is now thought to be imported into Europe each year to feed pigs, poultry, dairy and beef cattle, as well as farmed fish. The UK imports an estimated 140,000 tonnes of GM soya and as much as 300,000 tonnes of GM maize annually for use as animal feed.

In reality, say campaigners, this means that much of the meat and dairy products on sale are now produced from animals fed a GM diet. Much of the soya and maize used is grown in South America, including Brazil, Argentina and Paraguay.

In the UK, foods containing GM material for human consumption are currently required by law to be labelled. However, human foods derived from GM fed animals - meat, fish, milk and dairy products - do not need to be labelled. This represents a loophole, claim activists, which means consumers could inadvertently be eating be GM products.

Peter Melchett comments: "Labelling of all products from animals fed on GM should be legally required throughout the EU. Supermarkets in many European countries are now starting to label products from animals fed on GM."

"It is a scandal that UK supermarkets refuse to give this information to their customers, and instead deliberately keep them in the dark, with, at best, information on their websites and confusing answers to people who call their helplines. We know that people want accurate labelling, and at the moment supermarkets are betraying their customers on this issue."

The Soil Association cites a Food Standards Agency-published poll which found 67 per cent of the public thought it was important for products made from animals fed GM diets to be labelled.

In France, retail giant Carrefour in 2010 launched a labelling scheme to inform customers that animals used to produce foodstuffs have not been fed genetically-modified feed. More than 300 products now come with a 'free from GM feed' label after the supermarket giant said polls had found that more than 60 per cent of customers would stop buying products if they knew they were made from animals given GM feed.

Similar schemes are being adopted by other major European food retailers.

In Britain, tensions over the issue were heightened following the announcement earlier this year by four British supermarkets - Tesco, Sainsburys, the Co-op and Marks and Spencer - that they could no longer guarantee that the feed used in their poultry lines would be non-GM, citing their suppliers' apparently increasing difficulties in sourcing non-GM feed.

All said customers would continue to have non-GM options, including organic and certain premium ranges. Waitrose has continued to guarantee a non GM diet for its poultry, stating that it wants customers to have "choice".

British farmers are facing a dilemma - accept GM feed or go organic - according to some industry sources, who agree that conventional feed is increasingly becoming more difficult to source at an economically viable price.

They say that although the availability of non GM feed is disputed (producers organisations in Brazil maintain there is an ample supply of conventionally grown soya but say poor infrastructure at ports has held some shipments up) some major feed supply companies are now only offering their customers GM options, or organic.

"It's a nightmare trying to source non GM feed," a supermarket source said. "The reality is that trying to source it on the scale needed [by large retailers] is very difficult. The feed companies own the boats, the mills, they control the supply chain."

One UK feed merchant told The Ecologist that GM is now effectively being forced onto farmers: "As a farmer you are constantly under pressure, you are busy, you've got to be good at finance, a good production manager, so when someone offers [GM] feed that's cheaper, it's easy to say yes."

"Not having an option is not good. But when you've got an importer saying GM is fine and that he's not going to bring in [non GM] a farmer is not likely to go out and source his own."

The merchant said that not all farmers were aware about GM ingredients, and admitted some were not concerned anyway. He said some believed they were the victims of double standards: "'Why can we import GM from the USA or wherever, but are not allowed to grow it here' they say."

One Welsh organic dairy farmer agrees opinions are split: "I've got farming neighbours who are conventional; some are accepting GM with open arms, some don't want it. One milk supplier is not happy at all about GM feed," he says.

Michael Hart, a beef and lamb farmer from Cornwall, and the founder of the Small and Family Farms Alliance, says that he believes there is still demand for non GM feed but that it is becoming prohibitively expensive. "My local feed merchant says he can get organic, but for conventional non GM he'll demand more money."

Hart, a prominent anti-GM campaigner, says that since the BSE crisis farmers have become more sceptical about science and about what they are told, and that many have concerns about GM:

"Since 1996 farmers are more market aware and [more aware] of public opinion towards what we do. Is this GM stuff safe to feed my cows? Why do the public say they don't want it? Trust of science, trust of big business has gone."

Although not addressing the GM feed issue specifically, a poll conducted earlier this year by Farmers Weekly and Barclays Bank found that more than 60 per cent of British farmers would grow GM crops if it were legal to do so. The survey tested the opinions of more than 600 farmers across the UK.

Farm evidence "without merit"

Unofficially, one supermarket source admitted that "no one knows" when it comes to the potential health implications of using GM feed. As for whether GM is potentially risky or not, he says, "No-one can really put their hand on heart and say that one or the other is the case."

However, in formal replies to questions from The Ecologist retailers defended their position. A spokesperson for the Co-operative Group said:

"Since 2003, we have been working with suppliers to achieve greater availability of products from animals fed a non-GM diet. Unfortunately, this position is proving to be increasingly difficult to deliver.

"This is because the amount of non-GM soya being produced is decreasing, there are increasing difficulties in segregating through the soya supply chain and there is an increasing cost to farmers and potentially to customers for non-GM soya."

"All of this has meant that our previously stated position of increasing availability of products from animals fed a non-GM diet is no longer tenable."

The spokesperson said the company will continue to monitor the animal feed supply situation and added: "since this issue broke in the news we have had very few individual complaints and queries, and there has been no impact on sales."

Marks & Spencer said in a statement: "Alongside other retailers, we have written to our suppliers to tell them that we will no longer stipulate the use of non-GM feed in our fresh meat supply chain. This change in policy is absolutely necessary because there is now a much reduced supply of non-GM feed available to UK farmers. As such we can now no longer guarantee that our fresh meat has been fed on a non-GM diet."

Josephine Simmons from Sainsbury's said: "Whilst the latest scientific research and current Government advice is that GM ingredients do not present any risks to human health, we acknowledge the concerns of our customers and do not permit the use of GM crops, ingredients, additives or derivatives in any Sainsbury's own label food, drink, pet food, dietary supplements or floral products, this remains the case."

"We know that some people also have concerns about products from animals whose feed may contain GM ingredients. We therefore offer a choice of products from livestock fed a non-GM diet."

Tesco declined to comment.

The Food Standards Agency said it is "aware of anecdotal reports that pigs in Denmark perform much better when fed with non-GM than GM ingredients. These claims are unproven and they are currently being assessed by the Danish authorities. We look forward to their conclusions, and to the results of formal experiments that are under way in the Danish pig research centre (VSP)."

It added: "Every new GM crop must go through a detailed evaluation and be specifically authorised before it can be marketed. The evaluation covers safety and nutritional quality and is carried out at EU level by the European Food Safety Authority (EFSA). FSA is confident in the rigour of EFSA's assessments. As a result, the FSA can confirm that any GM food or feed that is authorised in the EU is as safe as its non-GM equivalent."

The body highlighted criticisms of both the Seralini and Carman research.

In a detailed statement, Tom Helscher from the agribusiness giant Monsanto - one of the world's largest producers of GM crops and suppliers of glyphosate, marketed under their well-known Roundup brand - said:

"Product safety and stewardship is a high priority for us and we routinely review studies that relate to our products and technologies. There is a large body of evidence that supports the food and feed safety of commercial GM crops and derived food and feedstuffs."

Helscher said the company were aware of Pedersen's claims but said that "if the allegations had merit, pigs all over Denmark and the US would be having diarrhoea problems, which isn't the case. There is a very robust collection of recent publications that found no negative effect of GM feed on pig health or performance."

He said Carmen's study and its results "are at odds with the long safety records of glyphosate and GM, and contrary to the weight of evidence substantiated by a large body of credible, peer reviewed literature."

"For over a decade, millions of pigs have been fed GM corn and soybean meal without negative impacts on health, reproduction, and growth. To date, there has been no scientific evidence confirming any detrimental impact on the animals or on the products - that is the meat, milk and eggs derived from animals fed GM crops.

"Therefore, the long history of safe use of GM feed is at direct odds with the author's allegations and suggests their findings are without merit."

Helsher said the Seralini study "does not meet minimum acceptable standards for this type of scientific research, the findings are not supported by the data presented, and the conclusions are not relevant for the purpose of safety assessment. Major flaws in the Seralini research have been reported by many reviewers."

Back in Denmark, Ib Pedersen's farm manager informs him that one of his pigs has unexpectedly died - the carcass has been carried out and lies behind the farm buildings, still warm.

Pedersen takes a sharp knife and slices the animal open, blood pouring onto the concrete floor. The intestines and other internal organs, including the stomach - it's full, the feed consumed just hours before is still visible - are pulled out and individually checked for signs of inflammation or other abnormalities.

Nothing unusual, the farmer says. Not this time.

*This article was updated on 14 / 12. The original had implied that the deformities in Ib Pederson's pigs were caused by GM feed; in fact, Pederson believes, it was glyphosate that was the cause of the deformities.*

Additional reporting & research: Sarah Stirk & Louisa Michel

Andrew Wasley is investigations editor of The Ecologist and the Ecologist Film Unit