This study examined the effects of aging on neuropeptide Y (NPY) and NADPH-diaphorase (NADPH-d)-positive neurons of the cerebral cortex in young (3 months) and aged (24 months) Fischer 344 rats by immunohistochemical and histochemical methods. In the aged group, the number of NPY-immunoreactive (IR)/NADPH-d-positive neurons was not significantly changed in all regions of the cerebral cortex compared to the control group. However, the number of NPY-IR/NADPH-d-negative neurons was significantly decreased in frontal association, primary motor, secondary somatosensory, insular, ectorhinal, perirhinal and auditory cortex in the aged group. In the aged rats, about 5-10% of NPY-IR/NADPH-d-positive neurons were dystrophic and scattered within the cerebral cortex. These results suggested that NPY-IR neurons that do not contain NADPH-d are affected by aging and that aging influences NPY-IR/NADPH-d-negative neurons in a region-specific pattern within the cerebral cortex of rats.