The increasing interest in the analysis of triglyceride (TG) species and the individual fatty acid (FA) composition requires expeditious and reliable quantification strategies. The utilization of flow injection analysis (FIA) coupled to quadrupole tandem mass spectrometry (MS/MS) for the simultaneous quantitation of TG and identification of FA composition facilitates the multiplexed verification of various biomarkers from small sample quantities. Enzymatic methods based on saponification and glycerol analysis are not suited for the determination of the FA distribution in TGs. This protocol proposes a procedure for the establishment of a relative quantitation method for middle- to high-abundance plasma TGs and the corresponding FA composition. Essential topics as FIA-MS/MS method development as well as sample preparation and validation strategies are described in detail.