The expression of Fos protein in the rat diencephalon, brain stem, cerebellum, and spinal cord was investigated using immunohistochemistry during chronic cold exposure, in order to clarify the neural regions involved in the thermoregulatory responses and the central mechanism of neural activation with cold acclimation. Numerous Fos-positive cells were observed in many brain regions after cold exposure and changes in the number of Fos-positive cells were analyzed quantitatively. Fos-positive regions were classified into three groups on the basis of the expression period of Fos protein. The first group was where a significant number of Fos-positive cells were seen 3 h and 24 h after cold exposure, but not observed 14 days after exposure; the regions included the lateral septal nucleus (LS), parvocellular paraventricular hypothalamic nucleus (pPVN), posterior hypothalamic area (PH), supramammillary nucleus (SuM), locus coeruleus (LC), dorsal tegmental nucleus (DTg), vestibular nucleus (Ves), and nucleus of solitary tract (Sol). The second group was where a significant number of Fos-positive cells were found 3 h, 24 h and 14 days after cold exposure; the regions included the preoptic hypothalamic area (POA), paraventricular thalamic nucleus (PV), lateral preoptic area (LPO), zona incerta (ZI), subparafascicular thalamic nucleus (SPF), lateral dorsal central grey (CGLD), lateral ventral central grey (CGLV), microcellular tegmental nucleus (MiTg), lateral lemniscus nucleus (LL), dorsal parabrachial nucleus (DPB), and the cerebellum. The third group was where Fos-positive cells were more numerous 14 days after cold exposure than they were after 3 h and 24 h of exposure; these regions included the ventromedial hypothalamic nucleus (VMH) and the spinal cord. These results demonstrate that the numbers and regions of Fos-positive cells in the rat brains changed during chronic cold exposure, and such changes may reveal the cellular adaptation of the thermogenic responsive neurons in the rat brain to cold acclimation.