More than 27 different gluten-free baked goods, including breads, cookies, pizzas and pies will be made at the renovated 8,000 square-foot bakehouse near Morrisville, North Carolina.
The move takes gluten-free goods a step closer to mainstream shopping aisles in the US, where many existing gluten-free products are only available on mail order, making it hard for consumers to access them easily.
"The new Whole Foods Market Gluten-Free Bakehouse will allow our stores to provide the widest selection of fresh gluten-free bakery items on the East Coast," said Ken Mayer, regional president for Whole Foods Market.
The idea behind the separate bakehouse is to prevent cross-contamination between gluten-free grains and ordinary varieties, a policy already followed by other gluten-free specialists such as Canada-based Glutino.
A gluten-free diet is medically necessary for people with coeliac disease, a hereditary illness which is essentially an intolerance to the gluten protein chains found in common grains such as wheat, rye and barley.
Awareness of coeliac disease, also known as nontropical sprue and gluten intolerant enteropathy, has increased in recent years as research has shown more people may be affected than previously thought - something which is likely to see a growth in the market for gluten-free products.
A recent study by the University of Maryland's Centre for Celiac Research claims that one in every 133 Americans may have coeliac disease, though it may take an important life event, such as surgery, childbirth or severe emotional stress to bring out symptoms.
And Teresa Jones, marketing manager for Whole Foods Market in North Carolina, said that the decision to create a gluten-free bakehouse had ultimately been led by consumer demand. "Customers at stores across the US were asking for the gluten-free products and our production couldn't keep up with the demand," she said.
"Coeliac is still one of the most under-diagnosed diseases but certainly the number of gluten-free products available has grown tremendously in the last few years," added Jones, who believes Whole Foods Market has an advantage as one of the few companies to sell fresh gluten-free products from its shelves rather than sending orders through the post.
The supermarket has also become something of a centre for coeliac sufferers by stocking products from other gluten-free specialists, such as US-based Authentic Foods, something which is helping the Whole Foods Market to corner the gluten-free retail niche.
The only problem, as Jones admits, is that gluten-free products "tend to be a little pricier because you use non-commodity ingredients to make them".
But coeliac sufferer Lee Tobin, also gluten-free team leader for Whole Foods Market and developer of the bakehouse idea, said the new bakehouse was a dream come true. "We are truly reaching out to this special population to offer flavourful, delicious foods they could not normally consume when made with traditional ingredients," he said.
Whole Foods Market currently stocks its own gluten-free goods at stores in North and South Carolina but with the help of the new bakehouse aims to expand availability to Virginia, Kentucky, Maryland, New Jersey, Pennsylvania and Washington DC by November.
The company, founded in 1980, has more than 160 stores in the US and is the world's leading natural and organic foods supermarket - and with stores also in Britain and Canada there is potential for its gluten-free baked goods to spread even further.