Schizophrenia (SZ) is a heterogeneous disease with a spectrum of symptoms, risk factors, and etiology. Abnormalities in mitochondria, the energy-producing organelles of the cell, have been observed in mixed cohorts of subjects with SZ. The purpose of the present study was to determine if striatal mitochondria were differentially affected in two different DSM-IV subgroups of SZ. Postmortem striatal tissue was examined from normal controls (NC), chronic paranoid SZs (SZP), and chronic undifferentiated SZs (SZU). Tissue was processed for calbindin immunohistochemistry to identify striosomal compartments, prepared for electron microscopy and analyzed using stereological methods. In both caudate and putamen, the density of mitochondria in the neuropil was decreased in SZP compared to both NCs and SZU. In the putamen, both the SZP and the SZU subgroups had fewer mitochondria per synapse than did NCs. When examining patch matrix compartments, striatal compartments associated with different circuitry and function, only the matrix exhibited changes. In the caudate matrix, the SZP subgroup had fewer mitochondria in the neuropil than did the SZU and NCs. In the putamen matrix, the SZP had fewer mitochondria in the neuropil as compared to NCs, but not the SZU. The numbers of mitochondria per synapse in both the SZP and the SZU groups were similar to each other and fewer than that of NCs. A decrease in mitochondrial density in the neuropil distinguishes the SZP from the SZU subgroup, which could be associated with the symptoms of paranoia and/or could represent a protective mechanism against some of the symptoms that are less pronounced in this subtype than in the SZU subgroup such as cognitive and emotional deficits. Synapse, 2012. © 2011 Wiley Periodicals, Inc.