Background: Soy contains phytoestrogens which are potent endocrine disruptors. Soy mainly contains phytoestrogens called isoflavones predominantly daizein and genistein. Main body: The present study determined the effects of isoflavones consumed post-weaning on prepubertal and postpubertal Leydig and Sertoli cell numbers, spermatozoa parameters and body weight to paired testicular weight ratio of Wistar rats. In this study, three diets were formulated containing different amounts of isoflavones. The diets were formulated by adding to the base diet different quantities of novasoy which is an isoflavone concentrate. The formulated diets contained 74.5, 235.6 and 1046.6 mg total isoflavones/kg pelleted diet, representing the isoflavones content less, equivalent or greater than that found in soy infant formula respectively. The results obtained showed that; administration of all doses of isoflavones significantly (p<0.05) increased Leydig and Sertoli cell numbers in both prepubertal and post pubertal rats as compared to the control groups. Administration of all doses of isoflavones significantly (p<0.05) decreased sperm count as compared to the control group. Administration of low doses (74.5 mg/ kg) of isoflavones significantly increased sperm motility as compared to the control group. Administration of moderate (235.6 mg/kg) and high (1046.6 mg/kg) doses of isoflavones significantly (p<0.05) increased sperm deformation as compared to the control group. Administration of moderate (235.6 mg/kg) and high (1046.6 mg/kg) doses of isoflavones significantly (p<0.05) increased body weight to paired testicular weight ratio as compared with the control groups. Conclusion Overall, the alterations brought about by isoflavones at all doses are indications of adverse effects on the male rat testicular function and this may adversely affect the functional capacities of the testes.