Serine palmitoyltransferase (EC 2.3.1.50) catalyzes the first unique reaction of sphingolipid biosynthesis. Activities were determined with different fatty acyl-CoA substrates to describe the range of long-chain bases that could be made by rat brain microsomes. The activities were greatest with palmitoyl-CoA and palmitelaidoyl-CoA, followed by fully saturated homologs differing from these by only one carbon atom, and diminished considerably as the alkyl-chain length increased or decreased, or with the presence of a cis-double bond. These characteristics explain the predominance of long-chain bases with 18 carbon atoms in brain sphingolipids, and account for the minor variants such as the C17- and C20-long chain bases.