1-Alkyl-sn-glycero-3-phosphate:acyl-CoA acyltransferase activity was found in six rat tissues: heart, spleen, brain, kidney, liver, and lung. The enzyme in rat brain showed highest specific activity in the microsomal fraction and its properties were studied in detail. Triton X-100 and bovine serum albumin were found to stimulate the activity of the enzyme. It was found that Triton X-100 affects the acyltransferase activity differentially depending on the acyl-CoA donor. Albumin reversed the inhibition caused by a high concentration of 1-alkyl-sn-glycero-3-phosphate. The enzyme was shown to be stereospecific in acylating the alkylglycerophosphate substrate. Only the 1-alkyl-sn-glycero-3-phosphate isomer, not the other optical enantiomer, was active with brain acyltransferase. Evidence is presented to show that this enzyme is different from 1-acyl-sn-glycero-3-phosphate:acyl-CoA acyltransferase. Investigations of the specificity of the brain acyltransferase activity for different acyl-CoA species (16:0, 18:0, 18:2, 20:4, 22:4, 22:6) showed a selectivity which was dependent on the alkylglycerophosphate concentration. At low 1-alkyl-sn-glycero-3-phosphate concentration the enzyme selected polyunsaturated acyl-CoA species over saturated species. Providing a low but continuous amount of 1-alkyl-sn-glycero-3-phosphate to the acyltransferase was accomplished by the in situ enzymatic reduction of alkyldihydroxyacetone phosphate with NADPH in the incubation mixtures. The acyl composition of ether-containing phosphoglycerides in rat brain microsomes, as well as the free fatty acid composition, was determined. Alkenylacylglycerophosphorylethanolamine contains a high percentage of 22:6 ester, and alkenylacylglycerophosphorylcholine contains a large amount of 16:0 ester. Comparison of the acyl-CoA specificity of 1-alkyl-sn-glycero-3-phosphate acyltransferase and ether/glycerolipid acyl composition suggests that this acyltransferase could partially determine the composition of acyl groups in ether lipids.