Converging lines of evidence support the view that autism is a disorder of brain connectivity in which abnormal brain structure and reduced coordination of activity across brain regions give rise to core features. The findings of functional connectivity MRI (fcMRI) and diffusion tensor imaging (DTI) studies of the brain are major sources of evidence for this theory. Although these techniques can illuminate brain connectivity in vivo, they are highly sensitive to head motion. Recent studies demonstrate that head motion can give rise to the patterns of abnormal connectivity that have been reported in children with autism. Thus, prior findings of brain connectivity abnormalities in autism may instead reflect motion artifact, and future studies must overcome this problem to be valid reflections of brain connectivity in autism. We propose to develop functional and diffusion MRI as a valid research tools for children with autism, without requiring sedation or anesthesia, by incorporating millisecond level motion detection and correction into faster pulse sequences, and developing an optimized data analysis pipeline. This will ameliorate a major source of artifact and speed the scanning process, thereby maximizing the chance of successful scans. These tools will benefit current and future studies of children with autism.