Background: Polycystic ovary syndrome (PCOS) is the commonest endocrine disorder in premenopausal women. This study aimed to evaluate the efficacy of isoflavonoids with clomiphene citrate during ovulation induction in PCOS women on the endometrial thickness which has an impact on pregnancy rate. Patients and methods: A prospective randomized clinical trial study was carried in Gynecology and Obstetrics Department, Zagazig University Hospitals on 160 infertile PCOS patients during the period from January 2019 to November 2019 to assess the effect of isoflavonoids in patients managed by clomiphene ovulation induction, triggered by HCG injection. All patients were divided into two groups: group I: included 80 women receiving Clomiphene citrate (CC) plus Isoflavonoids. Group 2: included 80 women receiving Clomiphene citrate only. Results: showed that the days till HCG injection were lower significantly in group I compared to group II which indicate better ovulation. As for the endometrial thickness, it was higher significantly in group I compared to group II. The number of ovulatory follicle(s) as single, two or three showed no statistical significant difference between the studied groups. The pregnancies number was higher significantly in group I where phytoestrogens were added to CC than group II. On the other hand, there was no statistical significant difference between the studied groups as regard the number of biochemical pregnancies between group I and group II. Conclusion: current results showed that Phytoestrogen (PE) (Isoflavonoids) with CC induced cycles, improved the endometrial thickness, promoted follicular maturation in a shorter time and also improved clinical pregnancy rates.