Background: Chlamydia trachomatis, Mycoplasma genitalium, and Ureaplasma urealyticum are genital infectious agents that can be sexually transmitted. They are involved in many infections both in women and men and can also be the cause of abortion in women. Objectives: This study aimed to determine the prevalence of the aforementioned bacteria in pregnant women and those with abortion in Kerman, southeast of Iran. Totally, 200 vaginal specimens were taken from pregnant women (n = 76) and those with abortion (n = 124) and were investigated for chlamydial and mycoplasmal infections using polymerase chain reaction (PCR) assay. Methods: From December 2015 to December 2016, 200 women were enrolled in this study. Demographic and behavioral information were gathered for statistical analysis. The prevalence of bacteria was determined in the vaginal samples by PCR. Results: All the studied bacteria were more frequently isolated from women with abortion, that is, 34.6% versus 15.7% for U. urealyticum, 20.9% versus 17.1% for M. genitalium, and 15.3% versus 10.5% for C. trachomatis. However, only for U. urealyticum the difference was significant (P = 0.0006). Again, occurrence of co-infection was mostly detected in women with abortion, and co-infection of U. urealyticum and M. genitalium was significantly higher (P ≤ 0.03). Also, follow-up studies indicated the importance of U. urealyticum in adverse outcomes of pregnancy in this region. Thus, special attention should be paid to this infection during pregnancy. Conclusions: The present study showed a significantly high prevalence of U. urealyticum in women with abortion separately and also in combination with M. genitalium. Diagnostic tests are recommended to detect these bacteria in high-risk women.