This study is the first of its kind to demonstrate that c-Fos immunoreactivity (ir) together with c-fos mRNA in their immediately adjacent tissue sections of a discrete brain region can be reliably measured. The c-fos gene expression in the paraventricular hypothalamic nucleus (PVN) of Sprague-Dawley rats for an animal model for visceral or somatovisceral pain induced by 2% acetic acid (AA) was used in this study. Specifically, c-fos mRNA signals were measured by quantitative autoradiography after in situ hybridization using c-fos oligodeoxynucleotide probe, and c-Fos-ir signals were represented by c-Fos immunostaining, as detected using c-Fos antibody in a regular immunohistochemistry. Signals from both c-Fos-ir and c-fos mRNA in the PVN were measured from their immediately adjacent cryostat sections. For the measurement of c-Fos-ir, it was carried out by reading 10 rectangles (1,000 μm2/rectangle) on each PVN section with c-Fos immunostaining. Specific signals were obtained from subtracting the nonspecific background signal from the total signals using a computer-assisted image analysis system. Results indicated that the AA treatment induced a significant increase of both c-Fos-ir and c-fos mRNA in the PVN. Interestingly, there was no increase of corticotrophin-releasing factor (CRF) mRNA expression in the PVN and central nucleus of the amygdala of Sprague-Dawley rats subjected to the AA treatment. In summary, this study has demonstrated that c-Fos-ir in the PVN with an anatomical resolution can be semiquantitatively measured after immunohistochemistry using an image analysis system, and that increased c-fos mRNA in the PVN 1 hr after the AA treatment is associated with no changes of the CRF mRNA expression. Anat Rec, 2007. © 2007 Wiley-Liss, Inc.