This study was performed to determine the effect of soy isoflavones on brain development and function in rats. Forty Sprague-Dawley male rats were provided diets containing different levels of soy isoflavones for 6 weeks; 0 ppm (control), 50 ppm (low isoflavone intake; LI), 250 ppm (medium isoflavone intake; MI) and 500 ppm (high isoflavone intake; HI). Learning ability was evaluated by a Y-shaped water maze and the activity of acetylcholinesterase in brain was assayed after decapitation. Food intake and body weights as well as weights of brain, liver, spleen, heart and kidney showed no significant difference among the four groups, which means 500 ppm of isoflavones is safe. In the water maze test, the frequency of error counted when rats entered one end of the alley without platform was significantly lower in the HI group than in the control group, and the escape latency as swim time taken to escape on the hidden platform was significantly shorter in the HI group than in the LI and control groups. The activity of acetylcholinesterase of the brain was significantly higher in the HI and MI groups than in the control group. Therefore, the results indicate that isoflavones may improve the cognitive function without adverse effects.