Cis- and trans-palmitoleic acids (Cis-POA and trans-POA) are isomers of palmitoleic acid, a monounsaturated fatty acid which affects glucose and lipid metabolism, and reduces insulin resistance. Trans-POA is used as a biomarker for indicating the risk of type II diabetes and coronary heart disease, but no methods of analysis or distinguishing between cis-POA and trans-POA have yet been reported.An accurate and precise HPLC method was developed to determine cis- and trans-POA simultaneously, and compared with results from a GC method. Cis- and trans-POA were analyzed by HPLC on a reverse-phase BDS-C18 column, equilibrated and eluted with acetonitrile (A) and water (B). In the established and validated GC method used for comparison, potassium hydroxide ester exchange was chosen to derivatize the cis- and trans-POA, before being determined.The calibration curves for cis- and trans-POA were linear over the range 0.05 to 500 μg/mL. The HPLC method exhibited good sensitivity, precision and accuracy. The limits of detection (LOD) for cis- and trans-POA were 0.2 and 0.05 μg/mL, respectively. The method successfully determined cis- and trans-POA in fish oil. For the GC method, the contents of cis-POA quantified were similar to those from the HPLC method, but the contents of trans-POA revealed significant variation between the two methods.After a comprehensive consideration of the characteristics of the saponification and methyl esterification methods which have been tested and verified, the HPLC method was found to be suitable for determining cis- and trans-POA contents in fish oil. It was also suggested that in natural fish oil, cis-POA may be in the glyceride state, and trans-POA almost completely in the free acid form. In comparison with the GC method, the HPLC method provided a simpler process and faster analyses for identifying and determining cis- and trans-POA. The study has also provided technical support for studying the pharmacological differences and relationship between structure and activity of cis- and trans-POA. This could help physicians to analyze patients' samples more quickly in 10 min and therefore provide a more rapid diagnosis of problems relating to the risk of type II diabetes and coronary heart disease.