Endometrioma surgery by stripping the cyst capsule has been associated with a reduction in ovarian reserve. It is still not clear whether the inflicted damage is immediate, sustained over time or associated with the use of electrocautery, nor which marker is more accurately reflects the post-operative reduction in ovarian reserve. This observational study assessed the damage inflicted by endometrioma removal with anti-Mullerian hormone (AMH) concentration and antral follicle count (AFC) pre and post-operatively. Twenty-five women with unilateral endometrioma underwent laparoscopic stripping of the endometrioma cyst capsule. There was a significant decrease both in AMH concentration (24%) and in AFC (11%) 1 month following surgery (P < 0.01). At 6 months post-operatively, the respective values were 24% and 15% less than preoperatively. AMH concentration and AFC showed no correlation with the use of bipolar electrocautery during surgery. Primordial follicles embedded adjacent to the cyst capsule were found in 61.5% of the specimens. Endometrioma surgery by stripping of the cyst capsule is associated with a significant reduction in ovarian reserve. The reduction is immediate and sustained over time. AMH appears to be a better indicator for post-operative quantification of the ovarian reserve. RBMOnline (C) 2013, Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.