By the statement "by the way they're built" I'll elaborate on the way they're genetically created.
Some diseases are more common in certain populations. For instance Tay-Sachs disease is seen more frequently in Ashkenazi Jews than the general population, assuming that they tend to marry within their group, that disease has more opportunities to pop up in the population.
If you look up Dalmatians, the genes that allow for the white coat under the spots also are responsible for deafness in the breed. If you consider that purebred dogs are bred with dogs of the same breed, diseases are more likely because there are consequences for wanting to maintain certain traits in the dog or build them a certain way.
If all dogs were allowed to breed indiscriminately, than the ones with less desirable traits would probably die off and dogs would probably move towards fewer breeds, but definitely healthier dogs.