Male Fischer 344 rats were either unirradiated or whole-brain irradiated with single doses of 10.83 or 17.16 Gy of X-rays at 4 months of age, and the organization of the DNA in permanently non-dividing cerebellar neurons examined as a function of age, dose and time after irradiation. In unirradiated rats and rats receiving a whole-brain dose of 10.83 Gy, there were no statistically significant changes in the organization of the bulk DNA and its association with the nuclear matrix as determined by: (a) the sensitivity of the DNA to digestion by micrococcal nuclease, (b) the sensitivity of the nuclear matrix-associated DNA to digestion by DNase I, (c) the relative DNA and protein content of undigested neuronal nuclei, and (d) the relative amount of DNA and protein that is tightly associated with the nuclear matrix after digestion with DNase I. In rats that were irradiated with 17.16 Gy at 4 months of age, there was a gradual decrease in the amount of nuclear proteins as a function of age (P less than 0.003). The amount of protein associated with the nuclear matrix in these irradiated aging rats was also consistently lower than that of their unirradiated counterparts (P less than 0.03). This decrease in the nuclear protein content of the cerebellar neurons in aging rats irradiated with 17.16 Gy may have caused a change in the overall organization of their neuronal DNA. Such a change in the organization of their neuronal DNA was indicated by a higher stainability of their bulk DNA by propidium iodide (P less than 0.03) and a higher sensitivity of the bulk DNA to digestion by m. nuclease (P = 0.087). Although these organizational changes in the neuronal DNA of aging rats irradiated with 17.16 Gy at 4 months of age are subtle, they might alter DNA repair processes or other neuronal functions that may be associated with the "natural" process of aging.