In higher functioning individuals with autism, a striking disparity exists between impaired social and emotional abilities and relatively preserved sustained attention and goal-directed cognitive abilities. As these two functional domains appear to map onto two distinct large-scale brain networks, the Task-Negative Network and the Task-Positive Network, respectively, we examined their intrinsically defined functional organization in individuals with autism. Using resting functional connectivity MRI (fcMRI), we found that, in autism, there was altered functional organization of the network involved in social and emotional processing, but no group difference in the functional organization of the network involved in sustained attention and goal-directed cognition. We suggest that these findings might serve to relate the seemingly disparate strengths and weaknesses of the autistic behavioral, perceptual, and cognitive phenotype into a tractable neurofunctional framework. These results also highlight the usefulness of resting fcMRI for studying the brain in neuropsychiatric and neurodevelopmental disorders.