Abstract Study question Considering the role of bacterial infection in causing endometriosis, we decided to compare the cultures of endometriosis-affected women a in this study Summary answer Considering the possible role of E. coli in the progression and/or recurrence of endometriosis and also infertility What is known already (5). Due to the finding of endotoxin of E. coli species in the peritoneal cavity and menstrual fluid of endometriosis patients, infection with this bacterium has recently been proposed as an effective factor in the occurrence and growth of endometriosis lesions. Study design, size, duration This prospective case-control study was carried out in the Women’s Department of Shiraz University of Medical Sciences in collaboration with the Bacteriology and Virology Department between 60 participants. Participants/materials, setting, methods 30 women with endometriosis in stages 3 and 4 of the disease, and 30 women without endometriosis who were candidates for surgery due to benign uterine diseases, underwent endometrial biopsy with Novak Kort in sterile conditions before starting their operation, and the results of their endometrial culture were analyzed and compared in terms of the presence of Enterobacter spp., Klebsiella spp., and E. coli species. Main results and the role of chance Based on the comparison between the two groups, only E. coli species had a significant association with the presence of endometriosis (P = 0.001). There was no significant relationship between the location of endometriosis in the pelvic cavity and culture results. Parity among the E. coli negative group was significantly higher compared to the E. coli positive group (P < 0.001). Limitations, reasons for caution Lack of sample trail for repeat testing and antibiotic susceptibility testing, low taxonomical resolution, and costly laboratory setup and maintenance are other limitations of this technology Wider implications of the findings we suggest that in women who have endometriosis and recurrent IVF failure and also in cases of endometriosis recurrence after surgical treatment, treatment of couples with appropriate antibiotics and repeated culture along with subsequent antibiotic susceptibility testing until their culture becomes negative could be beneficial. Trial registration number IR.SUMS.MED.REC.1400.097