Background: Chronic endometritis (CE) is a subtle pathology causing infertility and abnormal uterine bleeding. We evaluated the reliability of vaginal and cervical cultures for detecting infectious agents at the endometrial level. Methods: In a prospective diagnostic study, 181 women diagnosed with CE and 100 controls underwent vaginal, endocervical and endometrial sampling. Cultures for common bacteria, Neisseria gonorrhoeae, yeast and Ureaplasma urealyticum and PCR for Chlamydia trachomatis were performed. Results: The prevalent infectious agents at the endometrial level were common bacteria(59.7% of cases); U. urealyticum was detected in 11.0% and C. trachomatis in only 2.8%. The concordance rate between endocervical and endometrial specimens for common bacteria was 48.3%; 100% for C. trachomatis and 58.3% for U. urealyticum. The concordance rate between vaginal and endometrial cultures for common bacteria was 50.2%, only 16.7% for C. trachomatis and 48.8% for U. urealyticum. For common bacteria both vaginal and cervical cultures showed low sensitivities of 0.30 and 0.19, respectively. Conclusion: Common bacteria and U. urealyticum were the prevalent infectious agents in the uterine cavity of women diagnosed with CE. Both vaginal and endocervical cultures had low concordance with endometrial cultures. Only C. trachomatis test at cervical level had high concordance with endometrial findings.