To find out the correlation between pre-operative serum AMH and FSH levels and 3 months post-operative levels. The study was conducted in the Reproductive Endocrinology and Infertility Unit of Dhaka Medical College and Hospital (DMCH), Dhaka, Bangladesh, during July 2018 to December 2019. All admitted patients diagnosed with ovarian endometriomas (>4 cm) and of 20-35 years of age were included. Laparoscopy was the mainstay of surgery but in a few cases laparoscopy followed by laparotomy was done. Cystectomy (complete excision of the capsule) was attempted and adhesiolysis was also performed. Electrocoagulation was needed in few cases for haemostasis, which was performed by monopolar or bipolar diathermy. Carbon dioxide laser vaporization was not available, and cyst drainage was not done. In open cases, reconstruction of the ovary was performed. This study was a descriptive cross-sectional study. Initially for all patients, Serum AMH levels were measured preoperatively. Three months post surgery, Serum AMH was measured again, and data analysis and comparison of these values with ovarian reserve was done. Change in Serum FSH levels was also compared. Student’s t-test, paired and unpaired, were performed for different data. 69 patients were studied. 52.17% had tumours 4-6 cm, >6 cm in 47.83%. Tumour was bilateral in 36.23%. Laparoscopic cystectomy by monopolar cauterization was the 55.0% patients, laparotomy required in 10.14% patients. Average pre-operative serum AMH level in <29 yrs patients was 3.06±1.35 ng/ml, 2.38±1.54 postoperatively (p<0.001). For 30-35 yrs, they were 2.30±1.16 ng/ml and 1.39±1.01 ng/ml respectively (p<0.001). No significant difference in AMH was found in unilateral and bilateral cases (p=0.842), significant differences were found in pre- and postcystectomy AMH levels in these groups (p<0.001 for both). Pre and post-surgery FSH differences were very significant, p<0.001. When analysing the effect of different types of surgery we found that coagulation and excision both have negative effect on serum AMH levels, after 3 months (p<0.001). But there is no significant difference postsurgery between these two groups (p=0.0915). Surgery has a negative impact on ovarian reserve in patients with endometrioma, as evident by analysing different metrics and utilising student’s t-test.