As in all domestic mammals, sexual differentiation in dogs and cats starts early in the embryonic period prenatally and continues into early postnatal life. The result of such a process is, however, not evident until after puberty,a time when the entire reproductive system undergoes significant changes. Normality of sexual differentiation is difficult to observe in neonates of small animals, with the only gender difference being a slightly longer anogenital distance in male (13-15 mm) versus female (7-8 mm)animals. Early diagnosis of deviations from normality can spare breeders the time and effort devoted to raising an animal that may turn out to be unsuitable for becoming part of the reproductive stock and may spare owners the concern for a pet whose health may be unnecessarily threatened by failing to remove a malformed reproductive system early in life. This article reviews the incidence, clinical and gross anatomic features,and diagnostic approaches that veterinarians can use to address inborn errors of the reproductive system of dogs and cats, highlighting those malformations that bear clinical relevance and may become manifest from birth until puberty.