Hepatocyte nuclear factor (HNF) 4alpha, a transcription factor of the nuclear hormone receptor family, is generally expressed in some endoderm-derived epithelial tissues such as hepatocytes. In mice, an alternative promoter referred to as the P2 promoter is located upstream from the P1 promoter, resulting in the transcription of at least nine isoforms. In this study, we investigated the expression of Hnf4alpha in adult and embryonic mouse tissues, paying special attention to the developing metanephros by using immunohistochemistry and reverse transcriptase-polymerase chain reaction for the detection of P1 and/or P2 promoter-derived products. In adult mouse tissues, the kidney was the only organ expressing Hnf4alpha controlled only by the P1 promoter, and HNF4alpha was detected in the nuclei of epithelial cells in the proximal tubules, but not in other components of the nephron. In the metanephros, HNF4alpha was detected first at the epithelial cell nuclei in part of the comma-shaped body, distributed widely throughout the developing nephron and finally restricted to the proximal tubules. Interestingly, it was noted that Hnf4alpha mRNAs from stomach, pancreas and kidney tissues in embryonic periods were transcribed by both promoters. Immunohistochemistry for HNF4alpha and HNF1alpha revealed that both factors involved the same network of transcription factors, giving the impression that HNF4alpha was upstream of HNF1alpha.