Gender differences in brain structure and function have long been an interest to neuroscientists. One region where these differences have been reported is in the band of white matter that connects the two cerebral hemisphere, the corpus callosum. The current study explores the possibility that differences in cognitive ability contribute to the observed gender effects. The focus here is on visuo-spatial processing as measured by mental rotation which has also been found to have significant gender differences. The results reported show that two segments of the corpus callosum revealed gender differences, the rostrum and the anterior midbody. Both segments connect cortical regions that have been implicated in mental rotation. Additionally, the gender effect found in the rostrum appears to be due to visuo-spatial processing while the anterior midbody appears to be affected by both visuo-spatial processing and gender. These results suggest that because neural structure and cognition are intimately intertwined, cognition should be accounted for when making group comparisons of neural structure.