The objective of this study was to determine the effect of either 2.5 mg/kg Body Weight or 5 mg/kg Body Weight (BW) doses of isoflavones on semen quality, testosterone levels, lipid peroxidation and semen biochemistry of male New Zealand White rabbits. Animals were given both 2.5 mg/kg BW and 5 mg/kg BW doses of isoflavones. The tested doses were given to rabbits orally every other day for 13 weeks. Treatment with isoflavones caused an increase (p < 0.05) in libido (by decreasing the reaction time), sperm concentration, sperm motility (%), total motile sperm per ejaculate (TMS), packed sperm volume (PSV), total functional sperm fraction (TFSF), total sperm output, initial fructose concentration and normal sperm, while dead sperm was reduced compared to control animals. On the other hand, ejaculate volume, initial hydrogen ion concentration (pH) and plasma testosterone levels did not change in treated animals with both doses of isoflavones as compared to control. Concentrations of thiobarbituric acid-reactive substances (TBARS), total lipids, and low density lipoprotein were significantly (p < 0.05) reduced in seminal plasma of rabbits treated with either 2.5 mg/kg BW or 5 mg/kg BW doses of isoflavones. While, the activities of glutathione S-transferase (GST), lactate dehydrogenase (LDH), aspartate aminotransferase (AST), alanine aminotransferase (ALT), acid phosphatase (AcP), and alkaline phosphatase (AlP) were significantly (p < 0.05) increased in seminal plasma of treated animals. Also, total cholesterol, percentage cholesterol (out of total lipids), and high density lipoprotein were significantly (p < 0.05) increased, while triglyceride did not change in seminal plasma of treated animals. Supplementation at either level of isoflavones did not cause changes in live body weight (LBW), dry matter intake (DMI), and relative weights of testes and epididymis. The present results showed that either 2.5 mg/kg BW or 5 mg/kg BW doses of isoflavones caused an improvement of some semen characteristics and did not have negative effects on male fertility.