Tuesday the Supreme Court heard its first oral argument involving genetically modified crops (GMOs). Though the case, Monsanto Co. v. Geertson Seed Farms, has reignited the discussion over GMOs, or genetically engineered crops, it is still unclear what kind of impact the decision, which is expected by June, will have on the future of U.S. agriculture.

It all started in 2005, when the U.S. Department of Agriculture’s (USDA’s) Animal and Plant Health Inspection Service deregulated Monsanto’s Roundup Ready Alfalfa–otherwise known as a Finding of No Significant Impact–the agency did not prepare an Environmental Impact Statement, which environmental groups maintain is a violation of federal law. The agency did not place any limits on the planting, harvesting, or sale of the seeds.

In response, Geertson Seed Farms, along with The Center for Food Safety and a group of conventional and organic farmers, filed suit in federal district court, specifically citing violations of the National Environmental Policy Act, the Endangered Species Act, and the Plant Protection Act.

The discussion before the High Court this week (pdf) focused largely on whether that district court rightly issued a permanent injunction prohibiting the sale of Monsanto’s Roundup Ready Alfalfa until the Animal and Plant Health Inspection Service prepared an Economic Impact Statement.

The discussion this week did not really center on whether GMOs can contaminate, and thus irreparably harm, organic or non-GM, conventional alfalfa. During oral argument several of the Justices made it fairly clear the USDA should rule on that matter.

The USDA is set to issue an Environmental Impact Statement next year, which many expect will ultimately deregulate Roundup Ready alfalfa once again. Though, as Lawrence Robbins, the attorney representing Geertson told Justice Ruth Bader Ginsburg Tuesday,  “I think history remains to be written.”

Robbins painted a dire picture of the implications of deregulation: “[I]n a year, 6 months, whenever it is, people may have to get ready for a brave–for a–for a different world if not a brave new world.”

During the hearing, Justice Antonin Scalia made it clear that he views GMO contamination, or cross-pollination, in a much different light.

“This isn’t contamination of the New York City water supply,” said Scalia. “It’s the creation of plants of–of genetically engineered alfalfa which spring up that otherwise wouldn’t exist. It doesn’t even destroy the current plantings of non-genetically engineered alfalfa. This is not the end of the world. It really isn’t.”

“The most it does is make it difficult for those farmers who want to cater to the European market, which will not accept genetically engineered alfalfa, it makes it more difficult for them to have a field of 100 percent non-genetically engineered,” he continued. “But that’s not the end of the world.”

In his argument before the Court, Robbins maintained that the implications of deregulation will be significant.

“[I]t’s worth looking at that draft [Environmental Impact Statement], because it is very candid about how different the world will look,” he said. ” It tells us, we know this is going to shut down the–the export market. We know that the Japanese and the Koreans and Europeans won’t buy your products. We know this will hasten the consolidation of farming. We know it will hasten the demise–it will hasten the demise of organic farming, a rapidly developing business in this country.”

Monsanto maintains that the chances of GMO cross-pollination for alfalfa is extremely low.

“The district court’s suggestion that continued planting of [Roundup Ready alfalfa] could eliminate the availability of conventional alfalfa is bad science fiction with no support in the record,” the company wrote in its petition for review.

Until the Supreme Court issues a ruling, it’s impossible to know whether Monsanto v. Geertson Seed Farms will set an important precedent for the future of GMO regulation.

It is more likely that a ruling on whether or not the district court rightly issued an injunction to cure a National Environmental Policy Act violation will set precedent that could either help or hinder environmental protection groups’ ability to halt actions causing alleged irreparable environmental harm.