Assisted reproductive technologies allow mares to remain in training and produce offspring; however, limited data regarding the impact of exercise on folliculogenesis exists. Mares in training are reported to have reduced embryo recovery rates and ovulated smaller follicles. The objectives of this study are to evaluate the effect of exercise on folliculogenesis using ultrasound technology. Additionally, cortisol, luteinizing hormone (LH), follicle stimulating hormone (FSH) and estradiol concentrations in mares were evaluated. The exercise period was from April to September 2008 at Latitude: 34° 41' 1" N. Thirteen horses were assigned to Exercise (n=6) or Control group (n=7). Mares were exercised six days a week for 30 min; 10 min trot (4.0 m/s), 5 min canter (5.2 m/s), 5 min trot (4.0 m/s), 5 min canter (5.2 m/s), 5 min trot (4.0 m/s). Blood was collected prior to exercise, 30 min post exercise and in the afternoon every other day during diestrus and daily during estrus. Mares were ultrasounded transrectally daily using a 7.5 MHz linear rectal probe. Follicular growth was tracked and recorded. Serum was assayed for cortisol, LH, and estradiol using radioimmunoassay. Exercised mares experienced longer interovulatory intervals (P <0.05) and tended toward an increased time from deviation to ovulation (P =0.06). Exercised mares had altered follicular dynamics compared to Control mares. Mean cortisol concentrations were increased (P<0.05) post exercise in the Exercised group (6.29 ± 0.22 ug/dl in Exercised mares versus 5.62 ± 0.16 ug/dl in Control mares) indicating the Exercised mares were under increased stress. Maximum LH concentrations were lower (P<0.05) in Exercised mares (0.17 ± 0.06 ng/ml) than Control mares (0.41 ± 0.05 ng/ml). No differences were found in the mean, minimum, or maximum FSH concentrations between groups. Estradiol had a significant (P <0.05) group by cycle by day interaction with mean concentrations being higher in control mares on the days preceding ovulation. These data shows exercise alters follicular dynamics and hormone concentrations. Future research is needed to examine if these hormonal changes impact follicular growth and establish methodologies to retain normal ovarian function of mares in training and competition used in a breeding program.