Background: Endometriosis is one of the most common conditions causing infertility and an indication to undergo in vitro fertilization (IVF). High apoptosis rate and oxidative stress in patients with endometriosis are believed to negatively affect the IVF success rate. However, there have been conflicting results on the effect of endometriosis on IVF success, and there have been limited studies that directly assess endometriosis and its effect on oocyte quality. This study was performed to explore the correlation between mRNA BAX/BCL-2 expression and oocyte quality in endometriosis compared to non-endometriosis subjects. Methods: This was a cross-sectional study. 15 endometriosis and 15 non-endometriosis subjects were recruited through convenience sampling at Cipto Mangunkusumo Hospital, Jakarta. All subjects underwent follicle stimulation with recombinant follicle-stimulating hormone (FSH). Granulosa cells were collected and tested for BAX and BCL-2 expression and the results were compared to the oocyte quality and fertilization rate of the patients. Results: The total dose of recombinant FSH received by the endometriosis group was significantly higher compared with that of the non-endometriosis group (p = 0.005). There was a difference in BAX level (p = 0.029) and BCL-2 level (p<0.001) between groups. However, the BAX/BCL-2 ratio did not differ significantly (p = 0.787) between groups. No significant correlation was found between the BAX/BCL-2 ratio and any of the oocyte quality parameters measured. Conclusion: We found that there is a significantly higher dose in total dose recombinant FSH received by the endometriosis group compared with the non-endometriosis group. We also found that there was no significant difference in BAX/BCL-2 ratio between the endometriosis and non-endometriosis groups.