Autism is a psychosocial disorder clinically characterized by social difficulties, impairment in communication skills and repetitive behavioral patterns. Despite the increasing reported incidence of autism, the neurobiology of this disorder is poorly understood. However, researchers have uncovered numerous structural anomalies in the brainstem, cerebellum and forebrain of autistic individuals and there is substantial support for the association of hearing deficits with autism. In an effort to discover an anatomical correlate for the functional auditory deficits found in autism, we examined the SOC, a group of brainstem nuclei that function in sound source localization, in post-mortem brain tissue from autistic individuals. The neurons of the medial superior olive (MSO), an SOC nucleus, display a precise geometric organization essential for detection of timing differences between the two ears. We examined the architecture of the MSO in five autistic brains (ages 8 to 32 years) and two age-matched controls (ages 26 and 29 years) and found a significant disruption in the morphology of MSO neurons in autistic brains, involving cell body shape and orientation. The results from this study provide evidence on the cellular level that may help to explain the hearing difficulties associated with autism.