Endometriosis is a common reason for infertility and poor outcomes of assisted reproductive technology (ART). Inflammation is involved in the pathogenesis of this disease. The presence of microorganisms in women with endometriosis may increase levels of inflammatory markers. The purpose of this study is to determine the relationship between the presence of bacteria in the follicular fluid with the inflammatory markers of the complete blood count (CBC) and the outcomes of in vitro fertilization(IVF) in women with endometriosis. This case-control study was conducted on 74 patients undergoing IVF, referred to Al-Zahra Hospital in Rasht (Iran) in 2021. The patients were divided into two case groups including 37 women with endometrioma and the control group, including 37 infertile women with a male factor and normal ultrasound. In total, 74 follicular fluids were collected from the case and control groups and were cultured in the laboratory. The relationship between culture results with IVF outcomes and the levels of CBC inflammatory markers including the number of white blood cells (WBCs), lymphocytes, neutrophils, neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR), and platelet-to-lymphocyte ratio (PLR), erythrocyte sedimentation rate (ESR), and c-reactive protein (CRP) was analyzed. There was no significant statistical difference between the frequency of bacteria present in the follicular fluid (p = 0.861), the mean rate of fertilization (p = 0.363), the frequency of CRP (p = 0.999), and the mean WBCs, lymphocytes, neutrophils, NLR, LMR, and PLR in the two groups. There was a significant statistical difference between the mean number of oocytes of metaphase II (p = 0.034) and the mean ESR (p = 0.018) in the two groups. It seems necessary to evaluate follicular fluid as a biological substance that is considered an optimal factor for predicting oocyte quality, fertilization rate, embryo quality, and the success rate of ART.