ABSTRACTObjectiveTo evaluate whether the antral follicle count (AFC) is underestimated in the presence of an endometrioma.MethodsThis was a retrospective cohort study assessing all women undergoing in‐vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) at our clinic between January 2011 and December 2012 who had both ovaries and unilateral endometrioma. The primary outcome of the study was the difference between AFC and the number of oocytes retrieved per ovary.ResultsWithin the study period 787 women underwent IVF/ICSI at our clinic. Sixty of these women had at least one endometrioma, but 23 were excluded from the analysis as six had only one ovary and 17 had bilateral endometriomas. Therefore a total of 37 women were included in this study and analysis. Compared with the contralateral ovaries, ovaries with an endometrioma were significantly larger in volume (median, 10.3 (interquartile range (IQR), 4.7–18.9) cm3 vs median, 3.6 (IQR, 2.7–6.5) cm3; P < 0.001) and presented a significantly lower AFC (median, 3.0 (IQR, 1.0–6.0) vs median, 5.0 (IQR, 2.0–6.5); P = 0.001). However, the median number of oocytes retrieved was similar (P = 0.60) between ovaries with an endometrioma (2.0 (IQR, 0.5–5.0)) and the contralateral ovaries (2.0 (IQR, 0.0–4.0)). Accordingly, the median difference between AFC and number of oocytes retrieved was significantly smaller (P = 0.005) for ovaries with an endometrioma (0.0 (IQR, −1.0 to 1.5) than for those without (2.0 (IQR, 0.0–4.0)).ConclusionsAlthough the AFC is reduced in ovaries with an endometrioma, the number of oocytes retrieved is similar, suggesting that the AFC is underestimated in such ovaries. We believe that this is a consequence of an impaired ability to detect small follicles in the presence of an endometrioma. Copyright © 2014 ISUOG. Published by John Wiley & Sons Ltd.