The company made the announcement -- which makes it the first retailer in the country to require such labeling -- Friday at the Natural Products Expo West, a trade conference being held in Anaheim, Calif., The New York Times reported.
The action, which will be complete in five years, was in response to consumer demand, Whole Foods President A.C. Gallo said.
Products sold in Whole Foods market free of genetically engineered ingredients currently carry a label to that effect, as verified by the non-profit Non-GMO Project certification organization, he said.
"We've seen how our customers have responded to the products we do have labeled," Gallo said. "Some of our manufacturers say they've seen a 15 percent increase in sales of products they have labeled" as certified.
Gary Hirshberg, chairman of the Just Label It campaign for a federal requirement to label foods containing genetically modified ingredients, called the Whole Foods announcement a "game changer."
"We've had some pretty big developments in labeling this year, with 22 states now having some sort of pending labeling legislation," he said. "Now, one of the fastest-growing, most successful retailers in the country is throwing down the gauntlet."