The goal of this study was to use c-Fos immunohistochemistry to establish a rat model for studying the central projection of the esophageal afferent neurons during acid exposure. A cannula was placed in the esophagus of anesthetized Wistar rats with the tip approximately 2 cm above the lower esophageal sphincter (LES). Hydrochloric acid (0.1 N HCl, 50 mmol/L) with pepsin (3,200–4,500 U/mL), at pH 1.6, was then perfused into the esophagi of the experimental rats (n = 8) at 10 mL/hr continuously for 50 minutes. Normal saline solution (0.9% NaCl) was used in control rats (n = 6), and home cage control animals (n = 6) were given no stimulation. Thirty minutes after the perfusion, the rat was killed and the brain was removed and processed for c-Fos immunohistochemistry. A transverse section of the esophagus, 2 cm above the LES, was stained with hematoxylin and eosin stain for light microscopy. c-Fos immunoreactivity was significantly increased in a number of brain regions in the rats receiving the acid plus pepsin perfusion. These areas included the central amygdala, the Kölliker-Fuse nucleus, the nucleus of the solitary tract (NTS), the medial part of the NTS, the interstitial part of the NTS, the commissural part of the NTS, the paratrigeminal nucleus, the ambiguus nucleus, and the rostroventrolateral recticular nucleus. Perfusion with acid–pepsin solution also resulted in morphologic changes in the esophagus on light microscopy. This study suggests that acid plus pepsin perfusion of esophagus results in both neural activation in areas of the central nervous system and damage to the esophagus in an animal model.