Mutations in several genes have been shown to cause hypogonadotropic hypogonadism (HHG) in humans. This condition may result from abnormalities in hypothalamic gonadotropin-releasing hormone (GnRH) secretion, impaired pituitary gonadotropin release, or both. Here, we consider mutations in KAL in X-linked Kallmann syndrome; DAX1 in X-linked adrenal hypoplasia congenita; the related orphan nuclear receptor, steroidogenic factor-1; leptin and prohormone convertase-1, which may influence GnRH release and processing; the GnRH receptor; the pituitary transcription factors, HESX-1, LHX3 and PROP-1; and the gonadotropins, follicle stimulating hormone (FSH) and luteinizing hormone (LH). Identifying naturally occurring mutations in these genes provides important information about the role of these factors in the development and function of the hypothalamic-pituitary gonadal axis in humans. Different approaches to treatment and counseling may be needed, depending on the condition. Furthermore, the pathophysiological basis of HHG in the majority of individuals remains unclear, despite recent advances. Other candidate genes may be involved in these patients.