Purpose Collection of an endometrial specimen for investigating infectious agents in the endometrial cavity is an invasive technique that is at times difficult and painful. In order to avoid the need for endometrial sampling in the cases of suspected or evident endometrial pathology, the aim of this study is to investigate the reliability of cervical cultures for detecting infectious agents present at the endometrial level, comparing the results between cervical cultures and endometrial cultures in women with clinical signs of endometrial inflammation. Methods In a prospective diagnostic study, in the period from January 2009 to October 2010, we enrolled 404 women referred to the Department of Obstetrics and Gynecology for diagnostic hysteroscopy. All the patients underwent cervical and endometrial sampling. Cultures for common bacteria, Neisseria gonorrhoeae , yeast, and Ureaplasma urealyticum were performed. Results The most frequent infectious agents detected at the endometrial level were common bacteria, which accounted for 69% of all cases. In particular, streptococci were found in 27% of cases, and bacteria from intestinal flora ( Enterococcus faecalis and Escherichia coli ) was recovered in 31% of cases. U. urealyticum was detected in 10% and Mycoplasma in only one patient (0.2% of cases). No cases of N. gonorrhoeae were found. Conclusions Cervical culture has a low concordance with endometrial culture. In fact in only 33% of cases was the microorganism found in the cervix the same as that found in the endometrium. These results infer that an endometrial culture is a useful investigative tool for determining the microorganisms in endometrial pathology.