The transcription factor hepatocyte nuclear factor 4α (HNF4α) is a tissue specific transcription factor mainly expressed in the liver, kidney, intestine and the endocrine pancreas, but is also an essential regulator for early embryonic events. Based on its protein structure HNF4α is classified as an orphan member of the nuclear receptor superfamily. Comparing HNF4α transcription factors in the differentiated and dedifferentiated murine hepatocyte cell line MHSV-12 we identified in dedifferentiated cells the novel splice variant HNF4α7. This variant is characterized by an alternative first exon and has a lower transactivation potential in transient transfection assays using HNF4 dependent reporter genes. HNF4α7 mRNA and the corresponding protein are expressed in the undifferentiated pluripotent embryonal carcinoma cell line F9, whereas HNF4α1 only appears after differentiation of F9 cells to visceral endoderm. HNF4α7 mRNA is also found in totipotent embryonic stem cells. However, the function of HNF4α7 seems not to be restricted to embryonic cells as the HNF4α7 mRNA is also present in adult tissues, most notably the stomach. All these features suggest that the presence of distinct splice variants of HNF4α modulates the activity of HNF4α in a cell type specific way.