Puppy mills, as a general thing, have lots and lots of animals in a really small space. The dogs are crated almost all the time, and the crates are often too small for the dogs to do much more than turn around in. The dogs are often dirty, thin, and poorly muscled, as well as poorly socialized. Poor nutrition, poor sanitation, and poor vaccination protocols all combine to contribute to illness.
If you want to avoid puppy mills or backyard breeders (nearly as bad in a lot of cases, although they tend to have fewer animals), there are some really simple steps to take. Don’t buy from pet stores or through ads in the paper. Get referrals from other breed enthusiasts (the local rescue group for your preferred breed is usually a great place to ask around), and go to the breeder’s site. Look around, and ask questions. Ask to see all the animals, not just the puppies. If any of the animals seem to be living under conditions that aren’t what you’d want for your dog, or they refuse to show you some of the kennels, look elsewhere for your puppy. Ask to see their puppies’ veterinary exam and vaccination records. If the breeder says, “Oh, I vaccinate all my pups myself,” move along. Vaccines sold directly to breeders (through farm stores or catalogs) are often stored improperly, which makes them utterly useless, and there is no substitute for a vet exam to make sure your pup is healthy.