With very little exception, all puppies sold in pet stores come from puppy mills. Pet stores say that they only purchase pets from USDA approved breeders, but humane organizations have been saying for years that the USDA license is meaningless. (You can learn more about puppy mills and the USDA licensing from the Humane Society of the US and Best Friends.)
Last month, the USDA proved the welfare organizations to be right. Their Office of Inspector General released a report about the gross problems with the inspections and regulations of commercial breeders.