Fatty acids (FAs) are essential components of lipids and exhibit important biological functions. The analyses of FAs are routinely carried out by gas chromatography-mass spectrometry after multistep sample preparation. In this study, several key experimental factors were carefully examined, validated, and optimized to analyze free fatty acid (FFA) and FA profiles of triglycerides and phospholipids in serum or tissue samples. These factors included (1) methylation/transesterification reagents, (2) validation of internal standards, and (3) final step concentration of FA methyl esters. This new method was utilized to analyze FFAs and the FA profiles of triglycerides and phospholipids in the serum and liver from a recently established rat model of nonalcoholic steatohepatitis (NASH). In this model, rats were fed a 220 kcal kg (-3/4) day (-1) diet containing either 5 or 70% corn oil for 21 days using total enteral nutrition. FA compositions of the serum and liver were found to shift from a pattern dominated by saturated and monounsaturated FAs (C16:0/18:1) to one dominated by polyunsaturated C18:2 derived from dietary linoleic acid. Alteration of FA composition in liver after overfeeding of high polyunsaturated fat diets may contribute to the progression of pathological changes from steatosis to inflammation, necrosis, and fibrosis observed in NASH.