This pilot study assessed the effects of exercise and nutritional counseling on hormonal, menstrual, and reproductive function in women with polycystic ovary syndrome (PCOS). Twelve females with a clinical, biochemical, and ultrasonographic diagnosis of PCOS were randomly assigned to endurance and resistance exercise plus nutritional counseling (EN) or nutritional counseling only (N) for a period of 12 weeks. Anthropometry, resting metabolic rate (RMR), selected hormones, and ovarian follicle population were measured pre and post-intervention. Following the 12 week intervention, greater decreases in sum of 2 skinfolds (p = 0.002) and a greater increase in estimated VO2 max (p = 0.017) occurred in the exercise group. Significant decreases in waist girth (p = 0.001) and insulin levels (p = 0.03) occurred in both groups. Hormonal changes were not statistically significant; however, a trend towards an improved hormonal profile, specifically sex-hormone binding globulin (EN, 39% increase; N, 8% increase) and lutenizing hormone : follicle-stimulating hormone (LH:FSH) (EN, 9% decrease; N, 27% decrease) occurred in the absence of weight loss. These findings suggest exercise and nutritional counseling may benefit the metabolic and reproductive abnormalities associated with PCOS.