We employed voxel-based morphometry (VBM) to compare the distributions of grey matter found in structural magnetic resonance imaging (MRI) brain scans of patients with comorbid learning disability with schizophrenia, schizophrenia alone, learning disability alone, and normal controls. Our primary aim was to replicate a previous region of interest (ROI) finding that comorbids and schizophrenics belong to the same population. Nonparametric analysis in normalized space showed no significant differences in grey matter distribution between the comorbid and schizophrenia groups. Furthermore, this analysis showed significant grey matter reductions in the comorbid and schizophrenia groups when compared to the learning-disabled or the normal controls. Parametric analysis localized the significant grey matter reductions between the normal controls and the comorbid and schizophrenia groups to the prefrontal and temporal lobes. It also identified an area of increased grey matter, on the inferior aspect of the postcentral gyrus, in the learning-disabled alone compared to the other groups. Native space parametric and nonparametric analyses, based on modulation of the normalized scans, confirmed the similarity in grey matter distribution of the comorbid and schizophrenia groups. Results confirm the ROI finding that in native space the learning-disabled group possesses the least and normal controls the most grey matter for the cohort. An increase in the basal ganglia of patients with schizophrenia vs. the learning-disabled, probably attributable to antipsychotic medication, was identified in the native space analysis. The native space results did not however register statistically significant temporal lobe reductions found under normalized analysis between schizophrenics and normal controls. This may be attributable to minor physical anomalies (MPA) in the schizophrenic cranium. Overall, these VBM results replicate previous ROI findings and are compatible with the view that comorbid learning disability with schizophrenia is a severe form of schizophrenia, rather than a consequence of learning disability. VBM has the facility to compare grey matter distributions in this structurally diverse cohort.