Growth-retarded mouse (grt/grt) is a spontaneous mutant that is known as an animal model for primary congenital hypothyroidism caused by resistance to TSH signaling. The regional pattern of cerebral cortical hypoplasia was characterized in grt/grt mice. Ex vivo computed tomography (CT)-based volumetry was examined in four regions of the cerebral cortex, i.e., prefrontal, frontal, parietal and occipito-temporal regions, which were demarcated by structural landmarks on coronal CT images. A region-specific reduced volume of the parietal cortical region covering most of the somatosensory cortex was noted in grt/grt mice rather than in both heterozygous (grt/+) and wild-type (+/+) mice. We concluded that the cortical hypoplasia in grt/grt was seen in identical cortical regions corresponding to human congenital hypothyroidism.