In this study, we have developed and validated a simple, accurate and sensitive gas chromatography–mass spectrometry (GC-MS) method for simultaneous quantification of 18 fatty acids in rat serum, including both non-esterified (NEFA) and esterified (EFA) fatty acids, and subsequent analysis of fatty acid metabolic profiles. This novel method was used to evaluate the serum levels of fatty acids from vehicle- and acetaminophen (APAP)-treated rats. Serum levels of 7 NEFAs and 14 EFAs were significantly higher in APAP-treated rats 24 h after APAP administration at 1500 mg kg–1 when compared with vehicle-treated controls. Control and APAP-treated rats could be differentiated based on their metabolic profiles using two different chemometric analysis methods: principle component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA). More importantly, we identified the following NEFAs as potential biomarkers of APAP-induced liver injury: oleic acid (C18:1n9), linoleic acid (C18:2n6), docosahexaenoic acid (C22:6n3) and arachidonic acid (C20:4n6). The serum concentrations of C18:1n9, C18:2n6 and C22:6n3 were all positively correlated (r > 0.8; Pearson's correlation analysis) with the activities of alanine aminotransferase (ALT) and aspartate aminotransferase (AST). These results suggest that a novel targeted metabolomics method based on the metabolic profiling of fatty acids analyzed by GC-MS provides exact serum concentrations of fatty acids as well as a prospective methodology to evaluate chemically induced hepatotoxicity. Copyright © 2012 John Wiley & Sons, Ltd.