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Reductions in glial cell density and neuronal size have been described recently in major depressive disorder (MDD). Considering the important trophic influence of glia on neurons, we hypothesized that this glial cell deficit is more prominent close to neurons. In this investigation we have characterized neuronal and glia cytoarchitecture in prefrontal area 9 using spatial point pattern techniques and two-dimensional measures of cell size and density. In post-mortem brain tissue of subjects with MDD, schizophrenia, bipolar disorder (BPD), and normal controls (15 subjects per group), we examined the laminar location and size of all neurons and glial nuclei in a 500 μm wide strip of cortex extending from the pia to the grey–white matter border. In MDD, we observed reductions in glial cell density (30%; P=0.007) in layer 5 and neuronal size (20%; P=0.003) in layer 6. We also found that glial cell density (34%; P=0.003) was reduced in layer 5 in schizophrenia, while neuronal size was reduced in layers 5 (14%) (P=0.006) and 6 (18%; P=0.007) in BPD. The spatial pattern investigation of neurons and glia demonstrated no alteration in the clustering of glia about neurons between control and patient groups. These findings confirm that glial cell loss and neuronal size reductions occur in the deeper cortical layers in MDD, but provide no support for the hypothesis that an altered spatial distribution of glia about neurons plays a role in the development of these changes.