Human embryonic stem (hES) cells, located on the periphery of the colonies, express the neuroectodermal markers nestin and Tuj1, suggesting a prematurely differentiated subgroup of cells. Here, we report that ceramide, a bioactive sphingolipid, selectively eliminates hES cells differentially expressing nestin and Tuj1. In contrast, undifferentiated cells are resistant to the apoptotic effects of ceramide. Ceramide-resistant hES cells express higher levels of the messenger RNA for ceramide-metabolizing enzymes that convert ceramide into pro-mitogenic metabolites. Based on these findings, we conducted long-term studies to determine whether liposomal ceramide can be used to maintain undifferentiated hES cells free of feeder cells. We continuously cultured hES cells on matrigel for 4 months with liposomal ceramide in a feeder cell-free system. Human ES cells treated with liposomal ceramide maintained their pluripotent state as determined by in vivo and in vitro differentiation studies and contained no chromosomal abnormalities. In conclusion, our findings suggest that exposure to ceramide provides a viable strategy to prevent premature hES cell differentiation and to maintain pluripotent stem cell populations in the absence of feeder cells.