Fetal cells derived from pregnancy can persist in a woman's blood and tissues for decades and have been implicated in the pathogenesis of autoimmune disease. Transplantation studies based on donor sex mismatch suggest that circulating stem cells can lead to liver regeneration with donor-derived hepatocytes. However, male cells in female liver could derive from pregnancy. We investigated male cells in liver biopsies from women with sons and asked whether they were hematopoietic cells or hepatocytes. Fluorescence in situ hybridization for X- and Y-chromosomes with concomitant immunohistochemistry was employed to study 28 female liver biopsies: 14 with the autoimmune disease primary biliary cirrhosis (PBC), eight with Hepatitis C, and six with other diseases. Total male cells and those expressing hematopoietic (CD45) or hepatocyte (CAM-5.2) markers were quantified. None of the male cells were hematopoietic in origin, as shown by lack of CD45 expression. Instead, male cells with hepatocyte morphology expressing the hepatocyte marker CAM 5.2 were found in 25% of all biopsies (36% of PBC and 14% of others). Overall, male cells were found in 36% of female liver biopsies. Of the PBC livers 43% had male cells compared to 25% of Hepatitis C biopsies and 33% of others. There was a trend toward increased numbers of male cells in PBC compared to others (mean 1 per 30,000 host cells vs 0.17 in Hepatitis C and 0.35 in others). Thus, male cells found in livers of women with sons include cells that express hepatocyte antigens. Therefore, transplantation and stem cell differentiation studies using sex difference to conclude that donor cells regenerate liver may be confounded by fetal microchimerism. Whether fetal cells play a role in autoimmune diseases like PBC merits further investigation.