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In this review, we described the genes that encode an array of transcription factors, matrix proteins, hormones, enzymes and receptors that are expressed at multiple levels of the hypothalamic-pituitary-gonadal axis (HPG). In addition, we reported our experience in the identification and characterization of naturally occurring mutations in patients affected by HPG disorders, including hypergonadotropic hypogonadism and hypogonadotropic hypogonadism, isolated or associated with others pituitary hormonal deficiencies, and abnormalities of pubertal and sexual development. To date, fifteen distinct genes implicated with HPG axis development and function were identified: KAL, SF1, DAX1, LEPTIN, PC1, GnRH, GnRHR, HESX1, LHX3, PROP1, FSHR, LHR, LHb, FSHb and FGFR1. Most mutations identified in our cohort were described for the first time in literature and they frequently were associated with new clinical and hormonal aspects of the diseases. Characterization of the consequences of these mutations in in vitro studies have provided increased understanding of the structure and function of the proteins encoded by these genes. The combined clinical, hormonal and molecular diagnosis of HPG disorders have helped significantly to improve the knowledge and, consequently, the diagnosis and treatment of these patients.