Milkfat is a complex mixture of many diverse FA, some of which have demonstrated health benefits including anticancer properties. Attempts are under way to enrich milkfats with long-chain n-3 PUFA and CLA. It has been recommended that the analysis of these milkfats requires gas chromatography (GC) equipped with long, highly polar capillary columns. However, many analyses have been reported using CARBOWAX type (polyethylene glycol) capillary columns, such as SUPELCOWAX 10, even though the separation characteristics of many of the FA and their isomers present in milkfats have not been described in detail. This includes the isomers of CLA, cis- and trans-octadecenoic acid (18:1), linoleic acid (18:2n-6), and linolenic acid (18:3n-3), and the long-chain PUFA. On the other hand, the resolution of these FA and their isomers has been more fully described using the highly polar capillary columns, such as CP Sil 88 and SP2560 because of the improved resolution obtained using these polar columns. The present study was undertaken to characterize the separation of these FA present in milkfats using a 60-m SUPELCOWAX 10 column, to compare the results to those from a 100-m CP Sil 88 column, and to determine if these two columns could possibly serve to complement each other for the analysis of total milkfat. The advantages of the SUPELCOWAX 10 column were a better resolution of the short-chain saturated from their monounsaturated FA (MUFA) analogs, and a complete separation of the alpha-linolenic (18:3n-3) and eicosadecenoic acid (20:1) isomers. It also provided an alternative elution order of the linoleic (18:2n-6), 18:3n-3 and gamma-linolenic (18:3n-6) acid isomers. On the other hand, the CP Sil 88 column provided a better resolution of the CLA isomers, MUFA, the isolated cis and trans MUFA fractions, the PUFA, and many the 18:2n-6 and 18:3n-3 isomers. A complete analysis of milk lipids using the CP Sil 88 column required the prior separation of total FAME using silver ion-TLC. The results of the present study confirm that the 100-m highly polar capillary GC columns are mandatory for the analysis of milk lipids, and at best, the 60 m SUPELCOWAX 10 capillary column serves as a complementary GC column to provide different separations in certain regions based on its intermediate polarity.