BACKGROUND Urinary and recombinant synthetic gonadotropin analogues have been useful in a variety of clinical scenarios in reproductive medicine. They can be used as substitution therapy, stimulation therapy, regulation therapy and hyper stimulation therapy. Gonadotropin analogues are used as substitution therapy for endogenous gonadotropins in patients with Group I hypothalamic pituitary failure. Gonadotropin analogues are also used as stimulation therapy in patients with hypothalamic pituitary dysfunction. Gonadotropins can also be used as regulation therapy when the ratio of endogenous gonadotropins is altered as in women with polycystic ovarian syndrome. In in-vitro fertilization cycles, gonadotropin analogues are extremely useful for controlled ovarian hyper-stimulation therapy to increase the yield of oocytes. The aim of this review is to discuss the physiological rationale of gonadotropin use in controlled ovarian hyper stimulation. The factors that affect the choice and dose of gonadotropins in controlled ovarian stimulation are listed. The availability and efficacy of urinary and recombinant products are also discussed.