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Hemispherotomy is a treatment for drug-resistant epilepsy with the whole hemisphere involved in seizure onset. As recovery mechanisms are still debated, we characterize functional reorganization with multimodal MRI in two children operated on the right hemisphere (RH). We found that interhemispheric functional connectivity was abolished in both patients. The healthy left hemispheres (LH) displayed focal hyperperfusion in motor and limbic areas, and preserved network-level organization. The disconnected RHs were hypoperfused despite sustained network-level organization. Functional connectivity was increased in the left thalamo-cortical loop and between the cerebelli. The classification probability of the RH corresponding to a minimally conscious state was smaller than for the LH. We conclude that after hemispherotomy, neurological rehabilitation is sustained by cortical disinhibition and reinforcement of connectivity driven by subcortical structures in the remaining hemisphere. Our results highlight the effect of vascularization on functional connectivity and raise inquiries about the conscious state of the isolated hemisphere. Clinical outcomes of hemispherectomy for epilepsy in childhood and adolescence. Brain. 2003; 126(Pt 3):556-66. doi: 10.1093/brain/awg052. Funnell MG, Corballis PM, Gazzaniga MS. Insights into the functional specificity of the human corpus callosum. Brain. 2000; 123 ( Pt 5:920-926. doi: 10.1093/brain/123.5.920. Gazzaniga MS. Forty-five years of split-brain research and still going strong. Nature Reviews Neuroscience. 2005; 6(8):653-659. Gold L, Lauritzen M. Neuronal deactivation explains decreased cerebellar blood flow in response to focal cerebral ischemia or suppressed neocortical function.spherectomy for treatment of refractory epilepsy in the pediatric age group: a systematic review. A. The reorganization of sensorimotor function in children after hemispherectomy. A functional MRI and somatosensory evoked potential study.