The neural bases of gender differences in emotional, cognitive, and socials behaviors are largely unknown. Here, magnetic resonance imaging data from 336 women and 225 men revealed a gender dimorphism in the functional organization of the brain. Consistently across five research sites, women had 14% higher local functional connectivity density (lFCD) and up to 5% higher gray matter density than men in cortical and subcortical regions. The negative power scaling of the lFCD was steeper for men than for women, suggesting that the balance between strongly and weakly connected nodes in the brain is different across genders. The more distributed organization of the male brain than that of the female brain could help explain the gender differences in cognitive style and behaviors and in the prevalence of neuropsychiatric diseases (i.e., autism spectrum disorder). Hum Brain Mapp, 2012. © 2011 Wiley Periodicals, Inc.