OBJECTIVE To investigate blood flow velocity in the ovarian stromal artery and uterine artery in women with polycystic ovary syndrome (PCOS) and to correlate these velocities with clinical and biochemical parameters. METHODS A prospective study was carried out in 55 patients with PCOS and 42 age-matched women who did not have PCOS. Clinical, biochemical, and hormonal characteristics, and utero-ovarian Doppler ultrasound blood flow parameters were determined, and correlations between the parameters were evaluated. RESULTS Ovarian stromal blood flow was higher (P<0.01) and uterine perfusion was lower (P<0.01) in women with PCOS compared with women who did not have PCOS. Ovarian stromal artery pulsatility index (PI) was inversely correlated with levels of dehydroepiandrosterone sulfate (DHEAS) and insulin-like growth factor-1, and with the luteinizing hormone/follicle-stimulating hormone ratio. There was a positive correlation between uterine artery PI and DHEAS level. CONCLUSION Doppler analysis of the uterine and intraovarian arteries may provide additional information about the etiopathogenesis of PCOS and partly explain the clinical implications of the condition.