In recent years, a positive relationship between genital perfusion and fertility has been established; in species other than horses, uterine and ovarian perfusion was improved by exogenous estrogen but impaired by exogenous progestin. The goal of the present study was to investigate the effect of exogenous estrogen and progestin on uterine and ovarian blood flow in cycling mares. Five Trotter mares were examined daily during three estrous cycles. Mares were given no treatment, altrenogest (0.044 mg/kg BW) orally from Day 0 (ovulation) to Day 14 and estradiol benzoate (5 mg i.m.) on Days 0, 5, and 10, in three cycles, respectively. There was no difference ( P>0.05) in the length of untreated versus estrogen-treated cycles (22.8±1.3 days and 23.2±1.5 days, respectively), but cycle length was increased ( P<0.05) in progestin-treated cycles (26.0±1.2 days). To facilitate comparisons among cycles with different lengths, data from Days 0 to 15 (diestrus) and from Days −6 to −1 (estrus) were analyzed. Transrectal Doppler sonography was used to evaluate blood flow in both uterine arteries and in the ovarian artery ipsilateral to the preovulatory follicle during estrus and ipsilateral to the corpus luteum during diestrus. Blood flow was assessed semiquantitatively using the pulsatility index (PI); high PI values indicated high resistance and a low perfusion and vice versa. An immediate effect of treatments occurred only after the administration of estradiol benzoate on Day 0; uterine PI values decreased ( P<0.05) between Days 0 and 1 and estrogen-treated mares but increased ( P<0.05) at the corresponding time in untreated cycles. Mean PI values for the uterine and ovarian arteries during both diestrus and estrus were higher ( P<0.05) in estrogen-treated versus untreated mares. Furthermore, mean uterine PI values during diestrus and estrus were higher ( P<0.05) in altrenogest-treated versus untreated mares. Neither estrogen nor altrenogest treatments had a significant immediate effect on ovarian PI values. Compared to untreated cycles, mean ovarian PI values were elevated ( P<0.05) only in the estrus following altrenogest administration. In conclusion, exogenous estrogen and progestin both decreased genital perfusion in cycling mares.