The effects of selective breeding on dogs, and other living things (including plants), can often be negative. When breeding for a particular trait, humans necessarily restrict the gene pool that goes into a mating, because they will only use organisms with certain characteristics. The more an organism is exposed to strict selective breeding for very specific characteristics, the smaller the available gene pool will become. This small gene pool means that the characteristics of the organism being bred become concentrated, and the same traits will pop up over and over again with high frequency; this is called "breeding true." For example, the Beagle breeds true because each and every Beagle that is born will look a certain way and act a certain way, within a range, of course. Unfortunately, these "concentrated gene pools" also mean that there is an increase in genetic diseases.

Some breeds suffer much more from genetic diseases than others, and this is usually an indication of the quality of the breeding program that created them. In the past, not much was known about the specific details of genetics and inheritance and so breeders often simply took an apparently healthy, good-looking, efficient dog and bred it to another apparently healthy, good-looking, efficient dog. Not much thought was given to genetic conditions that weren't expressed or that developed later in life, after the dog reproduced. Nowadays, however, there is much more knowledge regarding genetics; indeed, screening tests have been developed for the more common genetic diseases. Reputable dog breeders have all their puppies undergo genetic screens to detect the presence of genetic conditions; they also test adults that are scheduled to be bred. If either puppies or adults are found to have a genetic disease, they are immediately scrapped from being used in the breeding program. There may be some exceptions for genetic conditions that aren't serious and/or for instances when the gene pool of a particular breed is extremely small.

Whatever the time period, though, one of the leading causes of the occurrence of genetic problems in a breed is popularity; the more popular a breed is, the more genetic problems it often has. This is because when a breed is popular, everyone wants one; people will start breeding dogs themselves, without thoroughly understanding genetics, and other individuals will start breeding dogs en masse so that they can turn a profit. In the quest for dogs that will satisfy the public, breeders like this will mate dogs without testing them for genetic conditions; and these bad genes will invade the gene pool. Reputable breeders have to work extra hard to keep the breed healthy under these conditions.

Fortunately for the Harrier, the breed has never become quite popular and breeders who were interested in this dog were extremely careful in their breeding programs. The individuals that existed were very healthy and matings almost always produced very healthy puppies; breeders were very careful in their decisions regarding which dogs to mate and only used the dogs with the best qualities. Today, this care has paid off. Occasional Harriers occasionally inherit diseases, but the incidence of genetic conditions is quite low for the breed, lower than the majority of other, more popular dogs.