The answer can be found here:

http://www.chipotle.com/en-US/fwi/fwi.aspx

–at least as far as Chipotle is concerned. Whenever possible, they use locally farmed produce and meat, and meat that was not fed hormones or antibiotics.

They’ve had their best success with pork. Since 2001, 100% of Chipotle’s pork has come from “naturally raised” pigs, who eat a vegetarian diet without antibiotics and live outdoors or in a deeply-bedded pen. Beef has been more challenging, but the company has used the weight of its large demand to lean on suppliers and push them to improve standards, to the point that 85% of the beef they purchase comes from farms that meet the company’s “naturally raised” standards. They won’t purchase any dairy from cows that have been treated with rBGH, or recombinant bovine growth hormone, to increase milk production, and they won’t buy chickens that have been fed antibiotics or other dangerous feed additives. Their goal is that one day soon all their meat and dairy animals will be pasture-raised.

Chipotle prefers to use organic produce, but is realistic about weighing the value of the “organic” label against the importance of sourcing produce from smaller farms that may follow organic-type practices but are not certified organic due to the required bureaucratic hoop-jumping. They also purchase produce locally as much as is practicable.

So the next time you, as a responsible consumer, have a craving for a burrito, patronize Chipotle over other burrito chains.