Unfortunately, the majority of toy breeds sold in pet shops likely come from puppy mill operations, which are, in effect, mass canine-production machines. The conditions in these places are not always sanitary for the dogs. Puppies are generally separated from their mothers at too early an age, and canine diseases often run rampant where lots of dogs are kept. Breed rescues regularly try to keep their breeds out of the hands of puppy mill operators, but it's frequently a losing battle.

Drawbacks

Dogs in puppy mills are bred for profit, not for the betterment of the breed. Most of the dogs used for breeding live out their lives in small cages, and their puppies do not receive the early socialization every pup needs to thrive. The pups are often taken from their mothers quite young (the tinier the puppies, the quicker they sell), and this shortens their socialization time even further. These pups can be extremely difficult to housetrain, as they have been forced to soil their living quarters by being kept in small cages.

Some of the dogs in pet shops also come from local backyard breeders. Because many of these individuals house more than one breed, and they are less than conscientious about breeding their dogs, pups sold as purebred Yorkies may in fact be crosses between Yorkies and some other toy dog breed. Even though you'll be paying exorbitant pet-shop prices, you might be bringing home a mixed-breed pup with no health guarantees.

Positives

The only time you should consider buying a puppy or adult dog at a pet shop is when the store hosts adoption events for rescue groups or local shelters. You still won't be able to obtain health guarantees or a solid background on the dog, but at least you'll be contributing to an effort to help dogs in need instead of boosting a pet shop's (and perhaps a puppy mill's) profits.