Agribusiness giant Monsanto was in the news this year for taking a patent case to the Supreme Court. Now it has racked up another patent win in the higher courts, but the win has come at a price.

In the Supreme Court case earlier this year, farmer Vernon Bowman was trying to create a second crop of genetically modified Roundup Ready soybeans without Monsanto's permission. In the federal appeal case decided yesterday, Organic Seed Growers v. Monsanto, a group of farmers banded together with a wholly different concern. They didn't want another generation of GMO crops for "free"; they wanted the opposite. These farmers want to keep their fields entirely clear of transgenic seeds.

This is an increasingly difficult task, since Monsanto's patented crops have come to dominate some parts of the food supply. The organic farmers estimate that 85 to 90 percent of US-grown soybeans, corn, cotton, sugar beets, and canola contain Monsanto patented genes. The farmers in this case don't want to be anywhere near the "free ride" Bowman was accused of seeking; rather, they're concerned about "contamination." The Roundup Ready trait makes soybeans resistant to the herbicide glyphosate, but it isn't valuable to them. These farmers oppose the use of glyphosate altogether.

Paradoxically, this position brought the organic farmers to the same place Bowman found himself: in court, contesting Monsanto's patents. With the help of the Public Patent Foundation, the organic farmers filed suit in 2011, arguing that 23 Monsanto patents related to the company's key transgenic crops were invalid and not infringed. Even as they shunned Monsanto products, these organic farmers were being damaged, their lawyers argued, because they were forced to "forgo growing [conventional] corn, cotton, canola, sugar beets, soybeans, and alfalfa, since it is widely known that those crops are currently under severe threat of transgenic seed contamination."

The farmers were forced to take "costly precautions" to avoid such contamination. They had seeds tested and created "buffer" zones between their farms and their neighbors to avoid patented seeds blowing into fields. Just the fear of an expensive patent lawsuit brought by Monsanto altered their farming. Between 1997 and 2010, Monsanto brought 144 infringement lawsuits and settled another 700 cases without litigation.

"At least one appellant declared that the fear of suit by Monsanto is the sole reason he refrained from cultivating organic corn and soybeans," noted the US Court of Appeals for the Federal Circuit, which ruled in favor of Monsanto yesterday.

Promise you won’t sue us

To that end, the farmers went to Monsanto in 2011 asking the company to waive any claim for patent infringement against them, in a written "covenant not to sue." Monsanto wasn't going to sign any such document. The company referred them to a statement on its website, which read:

It has never been, nor will it be Monsanto policy to exercise its patent rights where trace amounts of our patented seeds or traits are present in farmer's fields as a result of inadvertent means.

Monsanto's lawyer assured them that the company "does not assert and has no intention of asserting patent-infringement claims against your clients."

The organic farmers, unsatisfied, went to court anyway. Monsanto's history of "ruthless enforcement" gave them reason to be worried. The company investigated as many as 500 farmers each year, trespassing on to their land, they alleged. And the company's hundreds of legal actions over patented crops spoke for itself. They wanted a judge's order saying they don't infringe.

But the district court wouldn't hear the case, ruling that because of Monsanto's position there was no controversy that a judge could resolve.

On Monday, the appeals court agreed with the district court. But it did so while making clear that Monsanto would be legally bound by its promise to not sue over "incidental infringement" if transgenic seed or pollen blows onto a grower's land. "Taken together, Monsanto's representations unequivocally disclaim any intent to sue," the three-judge appeals panel held. The effect is similar to the "covenant not to sue" that the farmers originally sought.

When pressed about farmers who had greater than "trace amounts," Monsanto's lawyer hedged during oral arguments. Still, "Monsanto's binding representations remove any risk of suit against the appellants as users or sellers of trace amounts (less than one percent) of modified seed," the judges held.

The Supreme Court case didn't resolve this issue, since the high court "carefully distinguished Bowman's use of the patented soybean seeds from the situation of inadvertent infringement," the Federal Circuit judges noted.

The organic farmers who filed the case reacted to yesterday's ruling as a "partial victory."

"Even though we’re disappointed with the Court's ruling not to hear our case, we’re encouraged by the court’s determination that Monsanto does not have the right to sue farmers for trace contamination," Maine farmer Jim Gerritsen, president of lead plaintiff Organic Seed Growers and Trade Association, said in a statement. "However, the farmers went to court seeking justice not only about contamination, but also the larger question of the validity of Monsanto’s patents. Justice has not been served."

The statement also suggests that many of the farmers may be interested in filing lawsuits seeking damages over contamination of their lands by Monsanto products, either against Monsanto itself or against neighboring farms. "[T]he decision today allows farmers who are contaminated to sue Monsanto and Monsanto's customers for the harm caused by that contamination without fear of a retaliation patent infringement claim against them by Monsanto," stated the Public Patent Foundation (PubPat).