Structural deficiencies within the cerebellum have been associated with schizophrenia. Whereas several region-of-interest-based studies have shown deviations in cerebellar volume, meta-analyses on conventional whole-brain voxel-based morphometry (VBM) studies do not implicate abnormalities in the cerebellum. Since this discrepancy could be due to methodological problems of VBM, we used a cerebellum-optimized VBM procedure. We acquired high-resolution MRI scans from 29 schizophrenia patients and 45 healthy controls and used a VBM approach utilizing the Spatially Unbiased Infratentorial toolbox (Diedrichsen in Neuroimage 33:127-138, 2006). Relative to healthy controls, schizophrenia patients showed reductions of grey matter volume in the left cerebellum Crus I/II that were correlated with thought disorder (p < 0.05; one-sided) and performance in the Trail-making test B (p < 0.01). No cerebellar group differences were detected employing conventional whole-brain VBM. The results derived from the cerebellum analysis provide evidence for distinct grey matter deficits in schizophrenia located in Crus I/II. The association of this area with thought disorder and Trail-making performance supports the previously suggested role of the cerebellum in coordination of mental processes including disordered thought in schizophrenia. The failure of conventional VBM to detect such effects suggests that previous studies might have underestimated the importance of cerebellar structural deficits in schizophrenia.