The HOX genes coding homeodomain proteins have been suggested as a candidate molecular switch that determines the fates of cells during embryonic development and patterning. It is believed that a set of differentiation-specific HOX genes enter into a turn-on state during tissue differentiation, in contrast to stem cell-specific HOX genes that enter into a turn-off state. However, comprehensive data of expression profiles of HOX genes in human embryonic stem cells (hESC) and differentiated embryonic tissues are not available. In this study, we investigated the expression patterns of all 39 HOX genes in hESC and human fetal tissues and analyzed the relationships between hESC and each tissue. Of the 39 genes, 18 HOX genes were expressed in stem cells, and diverse expression patterning was observed in human fetal tissues when compared with stem cells. These results indicate that HOX genes could be main targets for switching of stem cell differentiation into tissues.