AbstractCitron kinase (CIT‐K), a ser/thr kinase, is required during neurogenesis for cytokinesis of neuronal precursors. Deletion of the cit‐k gene in mice (cit‐k−/− mice) leads to a severe malformative central nervous system syndrome characterized by microencephaly, ataxia, and epileptic seizures; affected mice die by the third week of postnatal life. We have used NADPH‐diaphorase histochemistry, immunostaining for calbindin, calretinin, parvalbumin, and glutamic acid decarboxylase 67 (GAD67), and histological staining to undertake qualitative and quantitative analyses of the morphology and distribution of interneurons in the barrelfield cortex of cit‐k−/− mice. By postnatal day 13, lack of CIT‐K results in profoundly altered cortical cell morphology: the infragranular layers are populated by large, binucleate interneurons bearing many more dendrites than in control mice, an anatomical profile that has also been reported for the cortex of humans with cortical dysplasias and epilepsy. Tessellation analyses reveal that a clustered distribution of interneurons is maintained in cit‐k−/− mice, but that their nearest neighbor distance is significantly increased, and thus their density is reduced; the overall number of interneurons is more dramatically decreased in the absence of CIT‐K than would be predicted on the basis of the reduced brain size of affected mice. This reduction of inhibitory γ‐aminobutyric acid (GABA)ergic neurons likely underlies the occurrence of epileptic seizures in the cit‐k−/− mice. Furthermore, the altered distribution of NADPH‐diaphorase‐positive interneurons could be responsible for an impaired coupling of cortical activity to blood flow, also affecting cortical growth and functioning. J. Comp. Neurol. 513:249–264, 2009. © 2009 Wiley‐Liss, Inc.