Background: Mullerian anomalies are relatively common and contributing to the problems of infertility and poor pregnancy outcomes. But their molecular pathophysiology has been insufficiently studied. On the other hand, polycystic ovary syndrome (PCOS) is found in nearly 80% of women with hyperandrogenism and also in 8%-25% of normal ones. It seems that anti-mullerian hormone (AMH) which inhibits the formation of the mullerian ducts in male increases in women with PCOS. Therefore, the aim of the study is whether PCOS is associated with mullerian anomalies. Methods: In this case-control study, 83 women with PCOS and 83 cases without PCOS were evaluated with transvaginal ultrasound (TVS) for the diagnosis of mullerian anomalies. The results of each group were compared with other groups. Results: In the PCOS patients, TVS revealed mullerian anomalies in the uterine cavity in 29 out of 83 women. Among 29 patients who had lesions in their uterine cavity, 27 cases had septate uterus and two had arcuate uterus. In the healthy women, TVS revealed 6 septate uterus and 4 arcuate uterus abnormality cases of the uterine cavity. There were significant correlation between polycystic ovary syndrome of the patients and the mullerian anomalies lesions (i.e. septate and arcuate uterus) which were seen in them. Conclusion: Mullerian anomalies were more common in women with PCOS and the most common anomaly was uterine septum. In fact, the present results revealed that it seemed a cause-effect relationship between the mullerian anomalies and PCO syndrome may in fact exist.