Alpha-methylacyl coenzyme A racemase (AMACR), a novel immunomarker for prostatic adenocarcinoma, has recently been shown to be expressed in a number of malignancies including colorectal adenocarcinoma. In the current study, 59 surgically resected primary small intestinal adenocarcinomas (34 ampullary and 25 non-ampullary) were immunohistochemically examined for AMACR expression and compared with 66 colorectal adenocarcinomas (including 24 secondary tumors involving the small intestine by direct extension or metastasis). The results show that no AMACR immunoreactivity was detected in normal-appearing small and large intestinal mucosa. While 41 of 66 (62%) colorectal adenocarcinomas exhibited a variable degree of cytoplasmic staining, only 1 of 25 (4%) non-ampullary and 2 of 34 (6%) ampullary small intestinal adenocarcinomas showed positive AMACR immunoreactivity (P < 0.0001). Interestingly, AMACR appeared to be less frequently expressed in mucinous or poorly differentiated colorectal adenocarcinomas when compared with non-mucinous or better-differentiated counterparts, suggesting an association with microsatellite instability status. These results extend our previous observations that small intestinal adenocarcinomas differ markedly from colorectal adenocarcinomas despite their morphologic similarity. The different AMACR expression patterns may not only provide an additional diagnostic tool in the distinction between adenocarcinomas of the small and large intestinal origins but may also shed light on further understanding of intestinal tumorigenesis.