Most breeders do not sell to pet stores because they want to meet the buyers in person. They care about their puppies and want to make sure they go to a good home. Also, most national breed clubs prohibit or discourage members from selling to pet stores. Pet stores turn their attention to puppy mills and commercial breeders. Puppy mills mass produce puppies in cruel and unsanitary conditions.

Unfortunately, most of the puppies for sale at pet stores come from puppy mills. Puppy mills are concerned with making a profit and are careless in their breeding practices. As a result, most are inbred and have congenital and hereditary conditions. Furthermore, puppies suffer from neglect and malnutrition before arriving at the pet store and will often present with illnesses that can be transmitted to other pets and humans. Pet stores do not test for medical problems and do not run checks on their breeders. According to the  Humane Society, puppy mill puppies commonly have neurological problems, eye problems, hip dysplasia, blood disorders, and Canine Parvovirus. Research also show a high occurrence for heart disease and respiratory disorders.

Puppies from puppy mills and commercial breeders are separated from their mothers and litter mates before they are six weeks old. As a result, they do not learn rules and boundaries when playing together. This includes bite inhibition, which is learning how hard to bite before cause harm. Removing them at a young age can also lead to fearfulness and anxiety. This often manifests in the form of aggression. In fact, a recent study compared over 6000 puppies from pet stores and noncommercial breeders. The results showed that puppies from pet stores tend to be significantly more aggressive. Soiling issues and difficulty training was also unfavorable for puppies found at pet stores. Other behavior problems include hyperactivity and excessive barking.

When puppies are removed from their pack at an early age they do not benefit from socializing with their litter mates during play. It is during this time that puppies learn to interact with members of their species. They also learn to interact with humans when being handled. This is not often the case with puppy mills and commercial breeders who tend to limit their interaction. As a result, pet store puppies tend to be overly shy or aggressive and may not play well with others.

Most pet stores let you return a puppy during a warranty period. If the puppy has health issues, it is likely euthanized.

Pet store puppies are kept in overcrowded spaces often covered in fecal matter. They are sold to pet stores where they are kept in cages and forced to go to the bathroom in their cage. This makes housebreaking them extremely difficult.

Pet stores have costs associated with overhead which drive up the price. Reputable breeders often cost less and provide healthier puppies. Pet store puppies will cost upwards of $1,000 on average. If a puppy does not sell, the price is lowered and is continued to do so as the puppy grows

Documentation requirements are avoided by pet store owners. Those with papers are thought to falsify pedigree information. Many use deceptive practices and loose terms to mislead buyers. There is no guarantee that you’re getting a purebred.