The aim of this study was to determine changes that momentary low pH with or without pepsin causes in gene expression in laryngeal fibroblasts. Cell cultures were established from human false vocal fold (FVF) and postcricoidal (PC) mucosae. Using a real-time polymerase chain reaction, we analyzed messenger RNA gene expression of growth factors (transforming growth factor beta1, vascular endothelial growth factor, fibroblast growth factor 2), matrix metalloproteinases (MMP-1, MMP-2), and decorin in normal media, pH 4 media, and pH 5 media with and without pepsin. The FVF fibroblast gene expression differed substantially from the PC fibroblast gene expression. No significant interaction effects for acid and pepsin were found in the FVF culture, but in PC cultures we found a significant overexpression interaction effect for vascular endothelial growth factor, fibroblast growth factor 2, MMP-1, MMP-2, and decorin. These results imply that PC tissue is more sensitive than FVF tissue to the noxious effects of gastric contents. Furthermore, there appears to be a synergistic effect for acid and pepsin exposure in the posterior larynx.