Observations from different fields of research coincide in indicating that a defective gamma-aminobutyric acid (GABA) interneuron system could be among the primary factors accounting for the varied clinical expression of schizophrenia. GABA interneuron deficiency is locally expressed in the form of neural activity desynchronization. We mapped the functional anatomy of local synchrony in the cerebral cortex in schizophrenia using a novel functional connectivity MRI approach. Patients with schizophrenia showed weaker local functional connectivity (i.e., lower MRI signal synchrony) in a set of cerebral cortex areas largely coinciding with the synchronization effect of the GABA agonist alprazolam and the cortical areas showing higher density of parvalbumin and somatostatin GABA interneurons in humans. Our results provide detail of the functional anatomy of synchrony changes in the cerebral cortex in schizophrenia and suggest which elements of the interneuron system are affected. The information could ultimately be relevant in the search for specific treatments.