Uterine and ovarian blood flow was investigated in four mares during two consecutive estrous cycles using transrectal color Doppler sonography. The uterine and ovarian arteries of both sides were scanned to obtain waves of blood flow velocity. The pulsatility index (PI) reflected blood flow. There were significant time trends in PI values of all uterine and ovarian blood vessels during the estrous cycle (P < 0.05). PI values did not differ between the uterine arteries ipsi- and contralateral to the corpus luteum or the ovulatory follicle. PI values of the uterine arteries showed a wave shaped profile throughout the estrous cycle. The highest PI values occurred on Days 0 and 1 (Day 0 = ovulation) and around Day 11, and the lowest PI values were measured around Days 5 and -2 of the estrous cycle. During diestrus (Days 0-15) PI values of the ovarian artery ipsilateral to the corpus luteum were significantly lower than PI values of the contralateral ovarian artery (P < 0.0001). No differences (P > 0.05) in resistance to ovarian blood flow occurred between sides during estrus (Days -6 to -1). In this cycle stage PI values decreased in both ovarian vessels (P < 0.05). During diestrus, high PI values of the ovarian artery ipsilateral to the corpus luteum were measured between Days 0 and 2, followed by a decline until Day 6 (P < 0.05). From this time on, the resistance to blood flow increased continuously until Day 15 (P < 0.05). The cyclic blood flow pattern in the contralateral ovarian artery was similar to that in the uterine arteries (r = 0.68; P < 0.0001). No correlations occurred between the diameter of the corpus luteum and the PI values of the ipsilateral ovarian artery (P > 0.05) during diestrus. During estrus, there was a negative relationship between growth of the diameter of the ovulatory follicle and changes in PI values of the dominant ovarian artery (r = -0.41; P < 0.05). PI values of the uterine arteries and of the ovarian artery ipsilateral to the ovulatory follicle were negatively related to estrogen (E) levels in plasma during estrus (uterine arteries: r = -0.21; P < 0.05; dominant ovarian artery: r = -0.35; P < 0.05). In diestrus, PI values of the dominant ovarian artery were negatively related to plasma progesterone levels (r = -0.38; P < 0.0001), but not the PI values of the uterine arteries (P > 0.05). The findings of this study show that there are characteristic changes in blood supply of the uterus and the ovaries throughout the equine estrous cycle. There are negative correlations between resistance to blood flow in the uterine and ovarian arteries and the plasma estrogen levels during estrus. In diestrus, there is a negative relationship between the resistance to ovarian blood flow and the progesterone levels.