Endocrine disruptors are chemicals that interfere with the body’s endocrine system and produce adverse developmental, reproductive, neurological, and immune effects in both humans and wildlife. One example of endocrine disruptor is phytoestrogen which is a group of naturally occurring compounds that have been reported to cause fertility problems in animals. The major phytoestrogen in soy products is genistein, which has potent estrogenic activity both in vitro and in vivo. Previous findings have demonstrated that the control of primordial follicle development and subsequent folliculogenesis appears to be mediated by local production and action of specific paracrine factors. Preliminary studies also have shown that steroid hormones like estrogen play a critical role in the onset of primordial follicle assembly. These findings led us to further look into the effects of genistein on estrous cyclicity and ovarian folliculogenesis specifically on pre-antral and antral follicular development including their possible effects on ovarian morphometry of sexually matured female albino rats. The objectives of the study was to determine the effects of genistein on estrous cyclicity and ovarian folliculogenesis specifically on pre-antral and antral follicular development including their possible effects on ovarian and uterine morphometry of sexually matured female albino rats. Furthermore, the study elucidated its effect on the apoptosis of granulose and theca cells resulting to follicular atresia. A total of 24 female albino rats approximately 2-3 months of age of almost the same size were used in this study. The treatments were: Control (T0) distilled water, 8 mg/kg body weight genistein (T1), 12.5 mg/kg body weight genistein (T2) and 16 mg/kg body weight genistein (T3). Estrous cyclicity was determined using vaginal cytology. The experimental animals were sacrificed after five weeks and their ovaries and uterus were collected. Ovarian tissues were subjected to Paraffin technique for tne microscopic examination. All data gathered were subjected to One-Way Analysis of Variance (ANOVA) and significant differences among treatments were analyzed using Least Significant Difference (LSD). Results showed an increased length of proestrus and estrus period in treated rats, metestrus on the first week of treatment and diestrus on the second week of treatment period. In terms of antral and preantral follicles, rats treated with genistein have greater mean number compared with the control and the mean number of non-atretic follicles was high in the control group and T4 . Genistein treated rats at 12.6 and 16 mg/kg body weight have greater mean number of pre- antral and antral follicles as compared with those treated at 8 mg/kg body weight and the control. Genistein in soybean has endocrine disruption effect by altering estrous cyclicity and ovarian folliculogenesis but it has no adverse effect on heart and respiratory rates as well as on body temperature.