Chipotle has gone GMO-free.

That means none of the ingredients will be genetically modified -- for its tortillas, rice, chips and salsa, and also in the marinades used to cook its meats.

"Chipotle is really showing that there's a better way to do fast food," Chipotle co-CEO Steve Ells told CNNMoney in an exclusive video interview. "They say these ingredients are safe, but I think we all know we'd rather have food that doesn't contain them.''

Embracing ingredients that have not been genetically modified is not an easy thing, and the process has been years in the making. Ells and and his team had to wait for new GMO-free crops to be planted and harvested.

All of Chipotle's restaurants are now using non-GMO corn, which goes into many ingredients. Chipotle has also switched its cooking oil from soybean oil to GMO-free sunflower oil and rice bran oil.

Its pork and chicken still come from animals that eat GMO-feed. Its beef comes from pasture-raised cattle. But Chipotle (CMG) is the first national fast food chain to go this far in removing GMO from its food.

GMOs are a hot button issue among the foodies. Supporters say genetically modified food is safe. But critics worry about the amount of pesticide found in GMO crops. Some 80% of the food consumed in the U.S. is genetically modified, according to the USDA.

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Chipotle's stance in the debate allows Ells to distance his restaurants even further from other fast food rivals. "This is in line with the way we cook at Chipotle, we use classical cooking techniques," Ells said.

Chipotle -- once partly-owned by McDonalds -- has always taken a different approach from its competitors, he said. So far the message is resonating with the public.

While McDonalds (MCD) and legacy restaurant chains watch sales plunge, Chipotle is one of America' big growth stories. It has doubled its number of restaurants in 5 years -- to 1,831 from 976. Over that same time, its stock has skyrocketed about 350%, while McDonald's gained 38%.

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Carnitas problem continues: The GMO announcement comes as the company continues to try to resolve issues with its pork suppliers. Chipotle took its pork carnitas off the menu in 500 restaurants after a supplier didn't meet its health standards.

Chipotle execs admitted the carnitas-less restaurants are losing customers, which is slowing sales growth. But they're confident customers will come back once pork returns to all its restaurants later this year.

Chipotle also announced a week ago that it will be raising steak prices 4% to 6% in the fall. Ells tells CNNMoney the new non-GMO ingredients won't increase menu prices.

He argues it's a step forward for fast food.

"We want to make the old fast food model irrelevant," Ells said. "We want to make great ingredients and classic cooking techniques accessible to everybody."