Introduction: Polycystic ovary syndrome (PCOS) is a complex endocrine and metabolic disorder associated with ovulatory dysfunction. Presently, little is known about the primary factors that initiate PCOS. Chamomile flowers are used in alternative medicine for its anti-spasmolytic and anti-inflammatory effects. Antispasmodic properties of chamomile ease menstrual cramps and lessen the possibility of premature labor. This medicinal herb also stimulates menstruation. In this study, we evaluated the effects of Chamomile alcoholic-extract on the biochemical and clinical parameters in a rat model of PCOS. Materials and Methods: Estrous cyclicity of 30 virgin adult cycling rats was monitored by vaginal smears obtained between 0800 and 1200 hours. After about 4 days, each rat received an i.m. injection of Estradiol Valerate (Aburaihan Co., Iran), 2 mg in 0.2 ml of corn oil, to induce PCO. Corn oil was injected to the rats in the control group. All the rats in the experimental group were evaluated for follicular cysts 60 days after the injection. Rats with PCOS were treated by multiple doses (25, 50, 75 mg/kg) of intraperitoneal injections of Chamomile alcoholic-extract for ten days. The data were statistically analyzed at a significance level of p < 0.05 by ANOVA, followed by the Student Newman-Keuls post hoc test. Results: The histological and hormonal results showed that Chamomile can decrease the signs of PCOS in the ovarian tissue and help LH secretion in rats (p < 0.05). Conclusion: The alcoholic-extract of dried Matricaria chamomilla L. flowers can not only induce recovery from a PCO induced state in rats, but also increase dominant follicles. Additionally better endometrial tissue arrangements can be regarded as another therapeutic effect of Chamomile.