Autism spectrum disorder (ASD) has been associated with a reduction in resting state functional connectivity, though this assertion has recently been challenged by reports of increased connectivity in ASD. To address these contradictory findings, we examined both inter- and intrahemispheric functional connectivity in several resting state data sets acquired from adults with high-functioning ASD and matched control participants. Our results reveal areas of both increased and decreased connectivity in multiple ASD groups as compared to control groups. We propose that this heterogeneity stems from a previously unrecognized ASD characteristic: idiosyncratic distortions of the functional connectivity pattern relative to the typical, canonical template. The magnitude of an individual's pattern distortion in homotopic interhemispheric connectivity correlated significantly with behavioral symptoms of ASD. We propose that individualized alterations in functional connectivity organization are a core characteristic of high-functioning ASD, and that this may account for previous discrepant findings.