Decay-accelerating factor (DAF, CD55), one of the membrane-binding regulators of complement activation, prevents host cells from the autologous complement-mediated attack. However, specific localization of DAF in the different layers of the digestive tract has not been defined. Using a crypt isolation procedure, we separated epithelium from the remnant stromal tissue and assessed the expression of DAF isoforms in the two layers in the guinea pig digestive tract. Both Northern hybridization and immunohistochemistry revealed DAF was preferentially expressed in the small intestinal epithelium compared to the stomach and colon. Reverse-transcriptase PCR demonstrated that the glycosyl-phosphatidylinositol (GPI)-anchored isoforms are predominant over the transmembrane (TM) isoforms in all digestive epithelium. However, there was no difference between GPI-anchored type and TM type in the stromal tissue. In conclusion, DAF was found to be primarily expressed in the small intestinal epithelium with isoforms differing between the epithelium and stromal tissue, suggesting differential roles in the guinea pig digestive tract.