Objective: To evaluate the change in the levels of anti-Mullerian hormone, adiponectin, weight loss and fertility parameters in obese women with or without polycystic ovary syndrome, following 12 weeks of supervised aerobic exercise. Methods: This study was conducted from August 2013 to October 2014 among obese women with or without polycystic ovary syndrome referred to Obstetrics and Gynecology clinic, Mansoura University Hospital, Faculty of Medicine, Mansoura, Egypt. Patients were classified into three age-matched groups; group A had controls, group B had patients with polycystic ovary syndrome and group C had obese women. Anti-Mullerian hormone, adiponectin, follicle-stimulating hormone, oestrogen, fasting insulin, fasting glucose, homeostasis model of assessment of insulin resistance, antral follicle count, hirsutism score, weight, menstrual cyclicity and ovulatory function were assessed at baseline and following 12 weeks of supervised aerobic exercise. Statistical analysis was performed using SPSS 17. Results: Of the 90 patients, there were 30(33.3%) in each group. The mean age was 28.7 +/- 3.84 years in group A, 27.9 +/- 4.1 years in group B and 27.6 +/- 5.7 in group C. The 30(33.3%) participants who responded to aerobic exercise interventions showed significant improvements in reproductive function), with lower baseline anti-Mullerian hormone levels, greater weight loss and higher adiponectin level compared to the the 30(33.3%) participants who did not respond to the exercise programme. Weight loss, fertility hormones, follicle-stimulating hormone, prolactin, oestrogen, antral follicle count, baseline anti-Mullerian hormone, and adiponectin were significantly correlated to the improvement in reproductive function (p<0.05 each). The change in anti-Mullerian hormone and adiponectin levels correlated significantly with physical activity level in both responders and non-responders (p<0.05). In women with anovulatory syndromes, there were significant improvements in ovarian process with an ovulation rate of 13(43.3%) and a restoration of menstrual cycle with a rate of 17(56.7 %) following 12 weeks of supervised aerobic exercise. Conclusion: Moderate aerobic training for 12 weeks had a positive significant effect on reproductive functions via modulating adiposity, the levels of adiponectin, anti-Mullerian hormone and fertility hormones.