In looking for a possible influence of nuclear inclusions (NIs) on neurodegeneration in human brains, we quantified morphological features of pontine neurons of three unrelated cases of neuronal intranuclear inclusion disease (NIID) and five control cases. Cross-sectional area of each neuronal nucleus and the indices for its deformity (long axis/short axis and circularity index defined as deviation from the perfect circle) were measured on pontine sections and their relation to NIs was statistically analyzed. Cross-sectional area of neuronal nuclei harboring ubiquitin-immunopositive NIs was significantly larger (110.6+/-1.6 micro m(2), mean +/- SE), while that of nuclei not harboring NIs was smaller (77.8+/-1.5 micro m(2)) than that in controls (90.5+/-0.7 micro m(2)). This difference remained significant even when the cross-sectional area occupied by NIs was subtracted from that of the nucleus harboring the NI (97.4+/-1.5 micro m(2)). This could hardly be explained if nuclear shrinkage is accelerated in the presence of NI. On the contrary, NI formation in pontine neurons of NIID might be linked, either directly or indirectly, to a mechanism, which counteracts rather than accelerates nuclear shrinkage. Because nuclear deformity was apparent even in neurons with NIs, whose nuclei were significantly larger than controls, the nuclear deformity is not secondary to its shrinkage and represents another aspect of neurodegeneration independent of nuclear shrinkage. Association of NIs to neurons of larger nuclear size in NIID brain indicates that NIs are not necessarily toxic to neurons.