Metabolism of free fatty acids(FFAs) is related to several important physiological events and therefore their quantitaion in biological samples arouses extensive interest and efforts. Existing gas chromatography with flame ionization detector(GC-FID) methods for the analysis of FFAs normally require derivatization of them in order to lower boiling points. But this extra procedure tends to induce additional error and it is laborious and time-consuming. A derivatization-free method was therefore established in the present investigation to determine FFAs in human plasma by capillary(GC-FID). After extraction of FFAs from plasma, a highly polar FFAP(free fatty acid in plasma) column was employed to directly quantitate FFAs concentration, free from derivatization reaction. All sample pre-treatments were carried out at room temperature, improving recovery of short-chain FFAs. Heptadecanoic acid(C17:0) was employed as internal standard, and the proposed method was validated for recovery, precision, sensitivity, stability, and linearity. Validation data show that it is suitable for clinical study that has been applied to the evaluation of FFAs levels in plasma of diabetic nephropathy(DN) patients during the course of treatment. Forty-seven patients diagnosed with DN were admitted to the double-blind experiment. Control group(n=17) underwent solely basic treatment and the patients did not show significant change in FFAs concentration during six months of treatment. Experiment group(n=30) was supplied with traditional Chinese medicine besides basic treatment. After six months of medication, their plasma concentration of palmitic acid(C16:0), stearic acid(C18:0) and oleic acid(C18:1n-9) decreased while linolenic acid(C18:3n-3) increased significantly(P<0.05). These four compounds could be served as biomarkers in the evaluation of drug efficacy, and their quantitation in plasma may provide additional information for disease progression in DN patients.