BACKGROUND AND PURPOSE: Functional reorganization of the brain can result from congenital brain disorders as well as from brain infarction. The purpose of our study was to use functional MR imaging to determine whether reorganization of brain function occurs in patients with schizencephaly. METHODS: Four patients with schizencephaly (three right-handed, one ambidextrous) presented with seizures. Associated lesions included agenesis of the corpus callosum (n = 1) and absence of the septum pellucidum (n = 1). Functional MR imaging was performed in each patient using a single-section fast low-angle shot (FLASH) blood oxygen level-dependent (BOLD) technique at 1.5 T in a standard head coil. The motor cortex was initially identified on an axial T1-weighted anatomic image. Thirty consecutive images were obtained during a motor task consisting of repetitive finger-to-thumb opposition. The percentage of change in increased signal intensity was calculated for the primary motor area. An ipsilateral activation index was used to compare the affected with the unaffected hemisphere. RESULTS: The percentage of change in increased signal intensity in the area of activation ranged from 4.8% ± 0.9 to 9.2% ± 1.2 (mean, 5.6% ± 1.5). The ipsilateral activation index in the affected hemisphere was 0.00 to 0.38, whereas that in the unaffected hemisphere was 15.4 to infinity. The difference in the ipsilateral activation index between each hemisphere was considered significant. CONCLUSION: Our results showed increased activation in the unaffected hemisphere in patients with schizencephaly, which may reflect functional reorganization of the motor area in patients with this congenital disorder.