For one, that cute little puppy most likely came from a large-scale, substandard commercial breeding operation, commonly known as a puppy mill. Puppy mills usually house dogs in overcrowded and often unsanitary conditions, without adequate veterinary care, food, water and socialization. The breeding stocks at puppy mills (possibly your new puppy’s mom and dad) are bred as often as possible in order to increase profits. Unlike your lucky puppy, the mom and dad will probably never make it out of the mill.

Hundreds of thousands of dogs suffer in puppymills in this country. They are prisoners of greed. The dogs are locked in small cages. They freeze in the winter and swelter in the summer. They never get out of their prisons. They are bred over and over again until they die. The only way to free them from their misery is to eliminate the demand for puppies by refusing to buy a puppy in a petstore and boycotting those stores that sell puppies. When the demand ends, the misery will end. The state and federal governments do not enforce the laws to protect the dogs. The commercial breeders and brokers have huge well-funded lobbying efforts. Please join this fight to free the prisoners of greed. The only person who is going to make a difference for these dogs is you. You, the people, can free them.

Harsh Realities
By buying a pet shop puppy, not only are you likely perpetuating and supporting a cruel industry, you—the consumer—run the risk of taking home a sick puppy! Dogs from puppy mills have been reportedly diagnosed with ailments such as respiratory infections and pneumonia, as well as hereditary defects like hip dysplasia. They may also be poorly socialized to people and other animals. Also, your new “purebred” puppy might not really be a purebred. Dogs at puppy mills are often bred indiscriminately, and lineage records are sometimes falsified to misrepresent that the dog is a purebred, when in fact, the animal is a mixed breed. Responsible breeders do not sell their dogs through pet stores.

The Laws Aren't Enough
Because a puppy mill is a business, the facility is designed purely for profit, not comfort. Laws are on the books to provide minimum-care standards for puppy-mill animals, but enforcement has historically been spotty at best. The U.S. Department of Agriculture (USDA) licenses and inspects puppy mills for violations of the Animal Welfare Act; likewise, some state laws are designed to protect the charges in the average puppy mill. But puppy mills can successfully navigate around these laws, whether by selling directly to consumers (thereby avoiding USDA licensing requirements) or simply by avoiding the reach of law enforcement (with so few USDA inspectors and minor fines, it's easy to stay in business).

How You Can Help
If you’re looking to make a puppy part of your family, check your local shelters first. There are so many amazing dogs who need homes. If your heart is set on a specific breed, keep in mind that one in four shelter dogs is a purebred. Additionally, you can do an Internet search for breed-specific rescue organizations. If those attempts still don’t give you the purebred puppy you’re looking for, you’ll need to learn how to choose a responsible breeder.

Also read this article from the HSUS.