Complete lecithin cholesterol acyltransferase (LCAT) deficiency is associated with fasting hypertriglyceridemia (HTG). We recently reported that, in ldlr-/-xlcat-/- mice, fasting HTG is associated with hepatic TG overproduction in association with an up-regulation of the hepatic srebp1 gene and altered expression of its target genes in lipogenesis and gluconeogenesis. We further investigated the role of hepatic polyunsaturated fatty acid (PUFA) metabolism in the modulation of the lipid phenotypes. In the ldlr-/-xlcat-/- mice, using the ldlr-/-xlcat+/+ littermate as controls, the hepatic level of cholesterol esters (CE) were reduced by 61.0 % whereas the 20:4-CE and 22:6-CE contents were each reduced by > 80%. In contrast, the hepatic levels of 20:4- and 22:6-containing phospholipid (PL) species were either unchanged or mildly elevated. Similar alterations of the hepatic PUFA in CE and in PL were also observed in the lcat-/- mice when compared to their wild type controls. In ldlr-/-xlcat-/- mice, hepatic mRNA level was markedly reduced for -6 desaturase (fads2) (70.2%) and acyl-CoA:cholesterol acyltransferase-2 (soat2) (57.0%). A similar pattern of gene expression change was also observed in the lcat-/- single knockout mice. In contrast, the acyl-CoA:diacylglycerol acyltransferase-2 (dgat-2) mRNA level was 1.7 fold up-regulated in the double knockout mice. In summary, we observed coordinated alterations in hepatic expression of the gene for fads2, soat2 and dgat2, resulting in a reduction in total hepatic PUFA pool and differentially in the PUFA-CE pool, in association with an increase in dgat2 gene expression for promoting TG synthesis and secretion. Some of the phenotypes are not readily explained by known mechanisms and may represent novel regulatory pathways.