Objectives: To determine the hormone profile during the menstrual cycle in women at sea level and at high altitude, and whether the time between the gonadotropin peak and ovulation is different at high altitude from that at sea level. Methods: The study was carried out in Lima (150 m) and Cerro de Pasco (4340 m), Peru. The hormone profile of 10 adult regularly menstruating women at sea level and 10 women at high altitude was assessed. Ovulation was identified by vaginal ultrasonography. Results: The pre-ovulatory follicle diameter was lower (P < 0.001) at high altitude than at sea level. Ovulation after LH peak occurred earlier at high altitude than at sea level. Serum FSH levels were higher at late luteal phase and early follicular phase at high altitude than at sea level (P < 0.05). The serum LH and FSH peaks were similar in women at sea level and at high altitude. During the early follicular phase serum estradiol levels were significantly higher at high altitude than at sea level (P < 0.05). During the late follicular phase the production of estradiol was higher at sea level than at high altitude (P < 0.05). The peak of serum estradiol was at day -1 in Lima and in day 0 at high altitude. At ovulation, the serum estradiol levels in women at sea level were 55.1% of the peak, but remained at high levels (80% of the peak) in women at high altitude (P < 0.05). The second increase of serum estradiol occurred earlier at sea level than at high altitude. From days +12 to +15, there was a significant decline in serum estradiol levels in women at sea level (P < 0.05) but not in those from high altitude (P > 0.05). Serum progesterone levels at days +5, and +8 to +12 were significantly higher at sea level than at high altitude. Conclusion: Our data suggest that hormone profile during menstrual cycle is different at high altitude than at sea level, probably as an effect of low barometric pressure.