Abstract Background Aim of this prospective, case–control study was to evaluate uterine arteries’ blood flow before and after laparoscopic surgery in patients with ovarian endometriosis and its possible correlation with infertility. Methods We prospectively enrolled 110 women of reproductive age; 69 with ovarian endometriomas and scheduled for surgery, and 41 controls. At enrolment, a detailed medical, gynecologic and obstetric history was collected. Fertility and pregnancy desire were assessed. All patients underwent complete physical and gynecologic examination. Transvaginal ultrasound with Doppler color flow was performed to evaluate Resistance Index (RI) of uterine arteries during the secretory phase, at enrolment (T0) and 3 months after laparoscopic surgery (T1). Results Among cases, 27 patients were excluded because they did not meet the inclusion criteria. At enrolment (T0) unilateral or bilateral flow alterations (RI ≥ 0.8) were found in 38 out of 42 patients with ovarian endometriosis (90%), whereas in the control group only 17 women (41%) had Doppler alterations. The difference in uterine artery RI values between cases and controls was statistically significant (P