Fatty acid-biosynthetic activity in rat liver cytosol fractions is much greater when the bivalent cation in the assay system is Mn2+ than when it is Mg2+. This difference between bivalent cations can be abolished if the cytosol fractions are preincubated with isocitrate and the bivalent cation for 30min before assay of fatty acid-biosynthetic activity. In a search for the biochemical basis of this phenomenon, the following differences between Mg2+ and Mn2+ were established: (1) Mn2+ promotes acetyl-CoA carboxylase activity of the protomeric form of the enzyme under conditions in which Mg2+ does not; (2) Mn2++ATP have little inhibitory effect on the polymerization of acetyl-CoA carboxylase whereas Mg2++ATP are markedly inhibitory; (3) under conditions in which utilization of malonyl-CoA in condensation reactions is prevented, the steady-state concentration of malonyl-CoA formed by a cytosol fraction is much greater with Mn2+ than with Mg2+. The role that each of these specific differences between Mn2+ and Mg2+ might play in causing liver cytosol preparations to have greater fatty acid-biosynthetic activity in the presence of Mn2+ is discussed.