Electrospray/tandem mass spectrometry was used to quantify lipid remodeling in mouse liver and plasma during inhibition of polyunsaturated fatty acid synthesis by the delta6 fatty acid desaturase inhibitor, SC-26196. SC-26196 caused increases in linoleic acid and corresponding decreases in arachidonic acid and docosahexaenoic acid in select molecular species of phosphatidylcholine, phosphatidylethanolamine, and cholesterol esters but not in phosphatidylserine, phosphatidylinositol, or triglycerides. For linoleic acid-, arachidonic acid-, and docosahexaenoic acid-containing phospholipid species, this difference was, in part, determined by the fatty acid at the sn-1 position, namely, palmitic or stearic acid. An understanding of phospholipid remodeling mediated by delta6 desaturase inhibition should aid in clarifying the contribution of arachidonic acid derived via de novo synthesis or obtained directly in the diet during inflammatory responses.