Inherited disorders of sexual development are important to identify as a cause of inherited infertility or sterility in humans and animals. Investigation of these disorders in dogs and cats can identify new mutations, allowing us to eliminate inherited disorders from breeding populations, while contributing to the understanding of mammalian sexual development and differentiation. This review updates an overview of normal mammalian sexual development while discussing disorders of sexual development at three consecutive levels, as errors in sex chromosome constitution, gonadal sex determination or phenotypic sexual development. The molecular mechanisms controlling sexual development and current molecular methods to identify causative mutations are illustrated in three specific examples of abnormal sexual development reported in small animals: XX sex reversal, Persistent Mullerian Duct Syndrome and cryptorchidism. Identification of causative mutations and development of practical tests to identify carrier and affected animals will provide effective mechanisms to reduce the prevalence of these disorders in small animals.