In recent years, gonadectomy in dogs has become the subject of growing criticism. Novel studies have demonstrated that this type of surgery can have negative effects on the dog’s health, effects that at first sight cannot be linked to the removal of the gonads or the absence of sex steroids. In this review, the literature on the long term-health effects of gonadectomy in dogs is described. The most important medical indication for ovariectomy in a bitch is lowering the risk of pyometra and mammary tumors, diseases which are prevalent in intact bitches. Spaying is often done in young bitches because of the protective effect it has on the development of mammary tumors. However, recent research has shown that orthopedical problems and some non-genital tumors are more prevalent in dogs after gonadectomy, especially if spayed before puberty. Results of these studies also show a major impact of the breed of the dog, hence a general advice for the dog population is not feasible. Veterinarians have to evolve towards a patient-specific advice in this matter.