Background The aim to find the morphological biomarker of disturbed activity of the orbitofrontal cortex (OFC) in depression was approached by the karyometric analysis of pyramidal neurons. Methods The study was performed on paraffin-embedded brains from 19 depressed patients from both major depressive disorder (MDD) and bipolar disorder (BD) diagnostic groups, including 9 suicides, and 24 matched controls. The karyometric parameters of medial OFC layer III and V pyramidal neurons bilaterally were evaluated by argyrophilic nucleolar organiser region (AgNOR) silver staining method. Results The enlarged nuclear area was found in layer V pyramidal neurons in the right OFC in non-suicides compared to suicides and controls, which was most likely the effect of neuroleptics. The intra-group comparisons between the hemispheres suggest the disturbed orbitofrontal lateralisation in depressed patients (predominantly in suicides) with moderate distinctness of the MDD and the BD diagnostic groups. Limitations A major limitation of this study is a relatively small number of cases. A further limitation is given by the lack of data on drug exposure across the whole lifespan. Conclusion The results suggest disturbed activity of OFC pyramidal neurons in depression, distinct in suicide and the diagnostic groups of mood disorders. The non-suicidal patients seem to benefit from neuroleptics, which most likely increase the activity of the subpopulation of OFC pyramidal neurons.