This had been a military town, built in 1954 to house a thousand people - research scientists and security personnel and their families - on an island in the Aral Sea. It was a secret base, known in authorised circles as Aralsk-7, not marked on any maps. This is because the Soviet Union was using the island for the open-air testing of biological weapons.

On the edge of town, we speed past a dump of rusting vehicles and other machinery with white stencilled cyrillic lettering still visible on some of the corroded flanks. The terrain here is uneven, a series of shallow craters. One of the hollows is full of discarded ammunition, the cases of shells and the ends of missiles poking out of the earth.

Abandoned in the early 1990s, after the collapse of the USSR, these are the forgotten remnants of the cold war. But not quite forgotten by all. Looters from the mainland, now part of independent Kazakhstan, make occasional trips to scavenge any useful scraps they can find in the desolate buildings. I had persuaded a group of these men to let me tag along.

Seclusion was key to the secret activities conducted in this out-of-the-way spot. Located 3,500km from Moscow, in the middle of a remote inland sea surrounded by sparsely populated desert deep in the heart of central Asia, the island was the perfect proving ground for a deadly array of airborne microbes. The name of this place, Vozrozhdeniye, appealed to me for its bitter irony. It means Rebirth Island.

The biological agents tested here included plague, anthrax and smallpox. These were the ones I'd heard of. The others had outlandish names - Q-fever, tularaemia, botulinum and Venezuelan equine encephalitis. Some had been genetically modified to make them resistant to existing medication.

The island had been chosen in part because of its geographical isolation. Fast patrol boats guarded Vozrozhdeniye against intruders throughout the decades of testing. The insular location also prevented the transmission of dangerous microorganisms to neighbouring mainland areas by animals or insects, and the surrounding stretches of water were considered wide enough to prevent biological agents being blown to the mainland.

Not any more. The waters of the Aral Sea have been receding for the past 50 years, sucked away by irrigation schemes. As its level has declined, the island has grown: in 1960 it was about 200 sq km; today Vozrozhdeniye is more than 10 times that size. In fact, it's now no longer an island. The Aral has shrunk so much that Vozrozhdeniye is today connected by a land bridge to the southern coast, in Uzbekistan.

Authorities in both Kazakhstan and Uzbekistan, which share the former island's territory, do not encourage visitors. Almost all of the agents responsible for the deadly diseases tested on Vozrozhdeniye are quickly destroyed when exposed to ultraviolet light. The island's sparse vegetation, hot desert climate, and sandy soil - which reaches summer temperatures of 60°C - all sharply reduce the possibility that pathogenic microorganisms can survive. The important exception is anthrax, a spore that outlives all the others. It can persist in soil for a very long time, and if any spores reach the lungs the chance of death is usually greater than 90%.

Britain harbours considerable expertise when it comes to anthrax, having conducted a few bioweapons tests on the Scottish island of Gruinard during the second world war. Gruinard remained uninhabited by government decree until 1988.

A US team visited Rebirth Island after September 11 2001, concerned that terrorists might find something useful, and ostensibly to clean it up. But nobody I spoke to before leaving for Kazakhstan knew exactly what the Americans had done. As one expert explained, it took more than 40 years to decontaminate Gruinard. "They pumped formaldehyde over the entire island. You have to kill every single spore, and they can live for centuries."

The US spending a mere few months on the Vozrozhdeniye clean-up wasn't good enough for him, so I was taking no chances. The looters looked me over with interest when I approached wearing a protective jumpsuit, rubberised overboots and a face mask. I proffered spare suits, brought along just in case, but there were no takers.

Weeds and straggling bushes line the concrete pathway past the chipped walls and broken windows of the derelict buildings. A battered road sign, the international one for children crossing, leans drunkenly as we pass what looks like a playground.

Doors hang limply from hinges, opening the way to interiors hacked to pieces by looters. In spite of the damage, the buildings still have the air of places that had been deserted in a hurry. Books lie open on the floors and pictures still hang on walls.

Down in the research zone, on a corridor in one of the laboratory buildings, rooms are full of electrical apparatus or equipped with work-benches and metal cages. One room contains a bed with the sheets still on. Above it a poster offers pictorial reminders of the importance of wearing all the necessary protective clothing. The sheets are rumpled, as if the occupant had risen one morning and forgotten to make his bed.

Back out in the sunshine, the gutted remains of a small building are still littered with petri dishes and glass test-tubes. It doesn't have a roof, and the rafters had been burnt but, scattered across the floor and in neat stacks along lines of metal shelving, most of the glassware is undamaged. There was no way of telling what foul concoctions they contained. So much for the clean-up operation.

Piled near a heap of test-tubes is a collection of wire contraptions. New weapons had been tested on horses, sheep and donkeys, but monkeys - our closest relatives - made the best subjects. These pieces of equipment look like their feeding trays.

Researchers at Rebirth Island used to joke that the condemned monkeys were the luckiest inhabitants of the Soviet Union because they lived on fresh fruit. Bananas, oranges and apples were rare delicacies for most human residents of the Soviet Union, but a test animal had to remain in prime condition right up to its last breath, usually taken strapped to a pole out in the killing fields just to the south of where we are. The cream of Soviet science, those who conducted the atmospheric trials, lived on hunks of bread and fatty sausage.

I stand still for a moment to listen. There are no sounds whatsoever. No birds, just an eerie silence. It is truly a deathly hush. Paradoxical for a place called Rebirth Island.

· To buy Nick Middleton's latest book, Extremes Along The Silk Road: Adventures off the world's oldest superhighway (John Murray, £20), for £18 with free UK postage, call Guardian book service on 0870 836 0875 or go to theguardian.com/bookshop