Ceramide (Cer) is a key intermediate in the synthetic and degradative pathways of sphingolipid metabolism, and is also an important second messenger. Natural Cer exists in the D-erythro configuration. Three additional, non-natural stereoisomers exist, but conflicting reports have appeared concerning their metabolism. We now compare the stereospecificity of three enzymes in the sphingolipid biosynthetic pathway, namely dihydroceramide (dihydroCer), sphingomyelin (SM) and glucosylceramide synthases, in subcellular fractions and in cultured cells. The L-erythro enantiomers of sphinganine, dihydroCer and Cer do not act as substrates for any of the three enzymes. In contrast, the diastereoisomer, L-threo-sphinganine, is acylated by dihydroCer synthase, and L-threo-dihydroCer and L-threo-Cer are both metabolized to dihydroSM and SM, respectively, but not to dihydroglucosylceramide and glucosylceramide. No significant difference was detected in the ability of SM synthase to metabolize Cer containing a short (hexanoyl) versus long acyl chain (palmitoyl), demonstrating that short-acyl chain Cers mimic their natural counterparts, at least in the sphingolipid biosynthetic pathway.