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The pathophysiology of infertility in endometriosis is still controversial and widely investigated. Several mechanisms are put forward. Whether In Vitro Fertilization-Embryo Transfer program is a solution still need further study. This research purpose is to compare the output of in vitro fertilization-embryo transfer between endometriosis infertility and non-endometriosis infertility. This a case-control study was followed by fifty endometriosis-associated infertility patients and fifty infertility due to tubal factor and or sperm undergoing In Vitro Fertilization-Embryo Transfer at Permata Hati Clinic, Dr. Sardjito Hospital Yogyakarta. The research output is fertilization rate, number of the good quality embryo and the success of pregnancy based on the pregnancy test. Data analysis was done by a statistical test of T-test and Chi-Square. Multivariate analysis was done by logistic regression. The number of good quality embryos in endometriosis group was lower (2.34 more or less 2.33 vs 3.44 more or less 2.97; p <0.05), but the fertilization rate was same (48.58 more or less 27.16 vs 55.19 more or less 30.9; p > 0.05). Compare to non-endometriosis, endometriosis group had bigger risk of pregnancy failure (OR 3.758, CI95% 1.11 until 12.68, p <0.03).