Though soybean isoflavones (SBI) have pharmaceutical properties, the compounds also have endocrine disrupting activities that may adversely affect fertility of mammals. The effects of SBI on metabolism, antioxidant capacity, hormonal balance and reproductive performance of male rabbits were investigated. Adult male rabbits (n = 21) fed an isoflavone-free diet were orally treated with 0 (control; CON), 5 (small; LSBI) or 20 (large; HSBI) mg of SBI/kg body weight/day for 12 weeks. Both SBI doses resulted in lesser blood plasma total protein concentrations, while there were no effects on glucose and cholesterol concentrations compared to CON. The HSBI-treated males had the greatest (P < 0.05) blood plasma total antioxidant capacity and least malondialdehyde. Treatment with both SBI doses induced a 43% increase in triiodothyronine concentrations (P < 0.05) and 82% in reaction times (P < 0.001), while decreased sperm concentrations (P = 0.01) and blood plasma testosterone concentrations (P = 0.017) 26% and 19%, respectively. The total functional sperm fraction was less (P < 0.05) in the HSBI group; however, there was no effect of the LSBI treatment as compared to values for the CON group. The kindling rates of females mated to HSBI-treated males tended to be less (P = 0.081) than those of does mated with LSBI or CON males. In conclusion, only the HSBI treatment improved antioxidant status; whereas, treatment with both LSBI and HSBI doses induced a hormonal imbalance which led to an impaired testis function indicating the sensitivity of the adult male reproductive system to SBI actions.