Joe Casey, a beer brewer by trade, was at an awkward place in his life. It was 2006, shortly after the birth of his first child, and his wife was diagnosed with celiac disease, the autoimmune disorder that’s triggered by the gluten protein found in grains such as wheat, rye, and barley. Barley, as in what a beer brewer uses to make beer. For a couple accustomed to sharing what Casey concocted each week on the job at Widmer Brothers, a Portland, Ore., brewery, the news, he says, “put a kink in our family dynamic.”
That same year he attended a presentation where he learned about something called Brewers Clarex. The product is an enzyme used to prevent chill haze, which turns beer cloudy, and Casey heard that it broke down gluten in order to do so. The thought of somehow removing gluten from a barley-based beer stuck in his mind for years. By the time he returned to it more seriously, he’d experimented with other ingredients, but none had passed the taste test. And his boss, then the CEO of Craft Brew Alliance (which owns Widmer), had also been diagnosed with celiac disease.
By 2012, Casey had transformed that idea into Omission Beer, a malt beverage he believes to be “gluten-free.” The results of gluten testing on each batch are posted online. Casey’s wife will now reach for a cold one. The brand’s handcrafted pale ale, lager, and IPA have been brisk sellers for the $192-million-in-revenue company. Omission even earned a stamp of approval (this past November) from the Celiac Sprue Association, known for some of the strictest gluten-testing standards in the country.
That’s when the gluten-free blogosphere erupted in alarm, doubting whether any traditional beer could be gluten-free. “I was really shocked and galvanized once I heard about the endorsement,” says biochemist Peter Olins, who runs the website UltimateGlutenFree.com. Writers at the Savvy Celiac and Gluten Dude were fuming as well.
The tempest is taking place in one of the fastest-growing specialty-food markets in the U.S., with companies including General Mills, Whole Foods, and Chobani crowding in. The growth has far outpaced regulators’ ability to draw up guidelines (the Food and Drug Administration only last summer defined “gluten-free” as less than 20 parts per million of gluten), as well as what is actually understood about gluten. Some 3 million Americans have celiac disease, and millions may grapple with non-celiac gluten sensitivity, a condition whose true cause is open to debate. Still others think skimping on gluten is “healthier.”
Some view Omission as an aggressive move into that market; others could not be more thankful it exists. Either way, the FDA so far isn’t convinced that claims to remove gluten from fermented products like beer can be measured. And Omission’s own regulator, the Alcohol and Tobacco Tax and Trade Bureau (TTB), agrees. The gluten-testing method the FDA views as scientifically valid for other foods (a “sandwich ELISA”) doesn’t work well on fermented or hydrolyzed gluten because the fragments are so small. Regulators still don’t think there’s a test to quantify gluten in malt beverages.
As for the Celiac Sprue Association’s approval, Casey is convinced that Omission made the cut because of additional testing the company submitted, utilizing an expensive technology called mass spectrometry. “We would not have been able to get their recognition seal without having that,” says Casey. (The association did not return Fortune’s requests for an interview.)
Dietitian Tricia Thompson, who runs a food-testing and research service called Gluten Free Watchdog, has tried to help people make sense of it all. She even wrote and posted a seven-page report on the debate online. But keeping the community calm isn’t easy. Says Thompson: “You have the strongest emotion in the celiac disease community around beer and pizza.”
This story is from the April 7, 2014 issue of Fortune.