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Background Myrrh (Commiphora myrrha (Nees) Engl.) has a long history of traditional use as a herbal medicine for different purposes. In ancient traditional Persian manuscripts, it has been noted that myrrh may act as uterine stimulant and probably cause complete abortion. However, there is no evidence to verify this comment. Therefore, the current study was carried out to evaluate the efficacy and safety of Myrrh in the treatment of incomplete abortion. Materials and methods In a randomized double-blinded placebo controlled clinical trial, 80 patients with ultrasound-documented retained products of conception (RPOC) were assigned to receive capsules containing 500 mg of Myrrh oleo-gum-resin or a placebo three times a day for 2 weeks. The existence of the retained tissue and its size were evaluated by ultrasound examination at the beginning and end of the study. Results After 2 weeks, the mean diameter of the RPOC in the Myrrh group was significantly reduced compared with the placebo group (P P = 0.01). The patients in both groups reported no serious drug-related adverse effects. Conclusion This study shows that Myrrh is effective and safe in the resolution of the RPOC and may be considered as an alternative option for treatment of patients with incomplete abortion. However, further studies on active compounds isolated from myrrh and their uterine stimulant effects are needed. Trial registration This study was retrospectively registered at Iranian Registry of Clinical Trials (www.irct.ir) IRCT code: IRCT20140317017034N7.