Background: The purpose of the study was to compare three-dimensional (3D) ultrasound semiautomatic antral follicle count (AFC) with two-dimensional (2D) ultrasound real-time AFC to evaluate patients with deep endometriosis and/or endometrioma submitted to ovarian stimulation (OS). Methods: This was a retrospective cohort study assessing all women with documented diagnosis of deep endometriosis who underwent OS for assisted reproduction treatment. The primary outcome was the difference between AFC by semiautomatic 3D follicle count using 3D volume datasets and 2D ultrasound count with the number of oocytes retrieved at the end of the cycle. The 3D ultrasound AFC was obtained using sonography-based automated volume count (SonoAVC), and the 2D ultrasound AFC data was collected from the electronic medical record. Results: Total of 36 women had deep endometriosis documented by magnetic resonance imaging, laparoscopy, or ultrasonography and 3D ovarian volume datasets stored from their first exam. The differences between the 2D and 3D AFC and the number of oocytes retrieved at the end of the stimulation were compared, showing no significant statistical difference between both methods ( P = 0.59). Correlations were similar using both methods when compared to the number of oocytes retrieved (2D [r = 0.83, confidence interval (CI) = 0.68–0.9, P < 0.001]); (3D [r = 0.81, CI = 0.46–0.83, P < 0.001]). Conclusion: 3D semiautomatic AFC can be used to access the ovarian reserve in patients with endometriosis.