Three children with middle fossa arachnoid cysts, presenting with non-specific symptoms and otherwise well, were investigated before and after surgery with magnetic resonance and 99Tc-hexamethylpropyleneamineoxime single photon emission computerised tomography scans, to assess the effect of the cysts on cerebral blood flow. All patients had evidence of a reduction in cerebral blood flow at presentation, even in the hemisphere contralateral to the middle fossa cyst, implied by perfusion defects seen centrally in the deep white matter of both cerebral hemispheres. After successful surgical excision of the cyst, the perfusion defects disappeared. This was associated with general improvement of pre-existing non-specific symptoms. These findings indicate that middle fossa arachnoid cysts may cause global impairment of brain function by interfering with its blood supply. This does not support the generally held view that such cysts are benign in nature when ‘asymptomatic’.