MIS, also known as anti-Mullerian hormone (AMH), a member of the TGFβ superfamily, is a product of granulosa cells and is expressed in females postnatally. Recently, data have suggested that MIS may reflect the size of the antral follicle pool, and therefore may be a useful marker of ovarian aging. Also, a few reports have suggested that MIS levels are higher in women with PCOS, but there is incomplete information regarding elevations when compared to age and weight matched controls, as well as relationships to ovarian morphology, levels of inhibin B (another putative marker of antral follicle health), and other reproductive hormones. Prospective observational trial in PCOS and matched controls. Fifty women with PCOS were recruited based on the classic criteria of chronic anovulation and hyperandrogenism. These women (age 25.8 ± 0.5 yrs; BMI 29.1 ± 0.9) were compared to 34 age (25.4 ± 0.8 yrs) and BMI (27.5 ± 0.6) matched ovulatory controls. Fasting blood was obtained in all subjects in the early follicular phase (days 5–6) after spontaneous or induced menses (in PCOS), as was vaginal ultrasound for assessments of ovarian volume and blood flow. Women with PCOS had higher LH (14.0 ± 0.9 vs. 9.1 ± 0.3 mIU/ml), testosterone (T, 103±7 vs. 43±3 ng/dl), and androstenedione (A, 3.6 ± 0.2 vs. 1.6 ± 0.1 ng/ml), as well as higher insulin (19.5 ± 1.2 vs. 7.3 ± 0.5 μU/ml) and lower QUICKI (0.31 ± 0.003 vs. 0.37 ± 0.003), p < 0.01. Ovarian volume was higher in PCOS (12.0 ± 0.9 vs. 4.7 ± 0.2 cc), and the pulsatility index was lower (1.4 ± 0.05 vs. 2.5 ± 0.1), p < 0.01. Inhibin B concentrations were higher in PCOS (70 ± 8.0 vs. 40 ± 3.4 pg/ml), as were MIS levels (6.7 ± 0.9 vs. 4.6 ± 0.5 ng/ml), p < 0.05. While inhibin B correlated directly with levels of MIS (r = 0.351, p < 0.01), inhibin B did not correlate with ovarian size or reproductive hormones, insulin or QUICKI. However, MIS correlated positively with ovarian size (r = 0.350, p < 0.05), LH (r = 0.312, p < 0.01), T (r = 0.280, p < 0.05), A (r = 0.389, p < 0.01), and estradiol (r = 0.281, p < 0.05), but MIS did not correlate with ovarian blood flow. In addition, MIS correlated positively with insulin (r = 0.249, p < 0.05) but not with BMI. Women with PCOS with the highest levels of MIS had higher ovarian volumes and values of LH, T, A, and insulin. These data suggest that MIS may be an important biochemical marker in PCOS and elevated levels may relate to the pathophysiology of the ovarian dysfunction.