Sphingolipids play a very important role in cell membrane formation, signal transduction, and plasma lipoprotein metabolism, and all these functions may have an impact on atherosclerotic development. Serine palmitoyl-CoA transferase (SPT) is the key enzyme in sphingolipid biosynthesis. To evaluate in vivo SPT activity and its role in sphingolipid metabolism, we applied homologous recombination to embryonic stem cells, producing mice with long chain base 1 (Sptlc1) and long chain base 2 (Sptlc2), two subunits of SPT, gene deficiency. Homozygous Sptlc11 and Sptlc2 mice are embryonic lethal, whereas heterozygous versions of both animals (Sptlc1^+/−, Sptlc2^+/−) are healthy. Analysis showed that, compared with WT mice, Sptlc1^+/− and Sptlc2^+/− mice had: (1) decreased liver Sptlc1 and Sptlc2 mRNA by 44% and 57% (P<0.01 and P<0.0001, respectively); (2) decreased liver Sptlc1 mass by 50% and Sptlc2 mass by 70% (P<0.01 and P<0.01, respectively), moreover, Sptlc1 mass decreased by 70% in Sptlc2^+/− mouse liver, while Sptlc2 mass decreased by 53% in Sptlc1^+/− mouse liver (P<0.001 and P<0.01, respectively); (3) decreased liver SPT activity by 45% and 60% (P<0.01, respectively); (4) decreased liver ceramide (22% and 39%, P<0.05 and P<0.01, respectively) and sphingosine levels (22% and 31%, P<0.05 and P<0.01, respectively); (5) decreased plasma ceramide (45% and 39%, P<0.01, respectively), sphingosine-1-phosphate (31% and 32%, P<0.01, respectively) and sphingosine levels (22.5% and 25%, P<0.01, respectively); (6) dramatically decreased plasma lysosphingomyelin (17-fold and 16-fold, P<0.0001, respectively); and (7) no change of plasma sphingomyelin, triglyceride, total cholesterol, phospholipids, and liver sphingomyelin levels. These results indicated that both Sptlc1 and Sptlc2 interactions are necessary for SPT activity in vivo, and that SPT activity directly influences plasma sphingolipid levels. Furthermore, manipulation of SPT activity might well influence the course of such diseases as atherosclerosis.