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Background: According to traditional herbal medicine, chamomile has been considered as one of the herbal remedies for patients with polycystic ovary syndrome (PCOS). The study aimed to investigate the effect of chamomile on lipid and hormonal parameters in women of reproductive age with PCOS. Materials and Methods: This study is a randomized clinical trial which was conducted on 80 women (40 patients in each group) of childbearing age with PCO. The intervention group received 370 mg oral capsules of chamomile three times a day for 3 months. The control group did receive starch capsule (three times a day). Hormonal and lipid parameters were examined before and 3 months after the intervention. Results: The mean age of the patients was 22.40 ± 5.10 and 24.38 ± 6.14 years in the intervention and control groups, respectively. Decreased level of testosterone was observed in the intervention group (in women with PCOS) who received chamomile capsules (P = 0.017). A significant difference was not seen in low-density lipoprotein cholesterol level (P = 0.249), high-density lipoprotein cholesterol (P = 0.073), triglycerides (P = 0.603), the hormone dehydroepiandrosterone sulfate (P = 0.423), and the ratio of luteinizing hormone/follicle-stimulating hormone (LH/FSH) in the experimental and control groups after the intervention (P = 0.420). Conclusion: According to the findings, oral administration of chamomile capsule caused a significant decrease in total testosterone levels in these patients. However, no significant change was reported with lipid parameters, the ratio of LH/FSH, and dehydroepiandrosterone sulfate level.