Temporal lobe arachnoid cysts are common findings during brain imaging. Debate exists regarding whether they result from temporal lobe agenesis or are a malformation of the arachnoid matter. We measured temporal lobe volumes in five children with left middle cranial fossa arachnoid cysts using morphometric analysis of magnetic resonance imaging scans. Three patients had neuropsychologic testing, and two patients had positron emission tomography scanning. All patients had significantly smaller left temporal lobes compared with the right side. On neuropsychologic testing two patients had cognitive deficits suggestive of left temporal lobe dysfunction. Temporal lobes adjacent to arachnoid cysts are smaller and less metabolically active when compared with the temporal regions on the opposite side. Patients with middle cranial fossa arachnoid cysts should undergo careful assessment of temporal lobe structure and function before any therapeutic intervention.