A simple approach for comprehensive profiling of fatty acids in human plasma based on gas chromatography-mass spectrometry (GC-MS) was described and validated. With this method, plasma fatty acid metabolic profiles of 23 coronary heart disease (CHD) patients and 25 healthy subjects were determined. Pattern recognition technology was used to establishing differences in the metabolic profiles of these two groups. Furthermore, CHD patients with two different patterns in Traditional Chinese Medicine clinical practices could be classified by the corresponding metabolic profiles, and several potential biomarkers were discussed.