Introduction: Formononetin is a phytostrogen found in plants such as red clover (Trifolium pratense), which has a chemical structure similar to the estradiol hormone. The aim of this study was to investigate the effects of formononetin derived from red clover on sexual dimorphic indices in mice during neonatal life. Materials and Methods: In this experimental study, male and female neonate mice were randomly divided into the control, vehicle and 3 groups (n=8) received formonetonin subcutaneously at doses of 5, 50 and 500 mg/kg body weight on days 1-5 after birth. After examining the puberty timing, parameters of estrus cycle, anogenital distance, sexual behavior, preferred saccharin and sex hormones were also investigated. The data were analyzed by SPSS statistical software and OneWay ANOVA test. Significance was shown at p values<0.05. Results: Puberty in females was significantly advanced by 500 mg/kg (p<0.01) and in male mice was delayed by 50 (p<0.05) and 500 mg/kg formonotonin (p<0.01). Mean duration of estrus cycle increased in 500 mg/kg formonotonin (p<0.05). Lordosis and mount numbers in 500 (p<0.001) decreased and the mean latency to the first mounts increased by 500 formonotonin (p<0.001). Percentage of saccharin preference increased by 50 (p<0.05) and 500 mg/kg formonotonin (p<0.01) in female mice. In addition, estradiol level in 50 (p<0.01) and 500 mg/kg (p<0.001) doces decreased and testosterone level in 500 formonotonin mg/kg (p<0.01) decreased, compared with controls. Conclusion: The results of this study show that the administration of formonotonin during the neonatal period of mice has the potential to cause development of sexual dimorphism parameters.