Hepatocyte nuclear factor‐4α (HNF4α) exists in multiple isoforms that are generated by alternative promoter (P1 and P2) usage and splicing. Here we establish monoclonal antibodies (mAbs) for detecting P1 and P2 promoter‐driven HNF4α, and evaluate their expression in normal adult human tissues and surgically resected carcinomas of different origins. Using immunohistochemical analysis, we demonstrate that, while P1 promoter‐driven HNF4α is expressed in hepatocytes, small intestine, colon, kidney and epididymis, P2 promoter‐driven HNF4α is expressed in bile duct, pancreas, stomach, small intestine, colon and epididymis. Altered expression patterns of P1 and P2 promoter‐driven HNF4α were observed in gastric, hepatocellular and colorectal carcinomas. HNF4α was expressed in lung metastases from renal cell, hepatocellular and colorectal carcinoma but was not observed in lung tumours. The P1 and P2 promoter‐driven HNF4α expression pattern of tumour metastases correlated with the primary site of origin. P1 promoter‐driven HNF4α was also found in intestinal metaplasia of the stomach. These data provide evidence for the tissue distribution of P1 and P2 promoter‐driven HNF4α at the protein level and suggest that HNF4α may be a novel diagnostic marker for metastases of unknown primary. We propose that the dysregulation of alternative promoter usage of HNF4α is associated with the pathogenesis of certain cancers. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.