This study examines the effect of the column operating temperature of 100 m SP-2560 and CP-Sil 88 capillary gas chromatographic (GC) columns on the separation of cis- and trans-octadecenoic (18:1) isomers in partially hydrogenated vegetable oils. The overlapping GC peaks were measured at column isothermal temperatures of 170, 175, 180, 185, and 190 degrees C. With both columns, isothermal operation at 180 degrees C produced the fewest overlapping peaks of the cis and trans isomers. At this temperature, all trans-18:1 isomers, except 13t-18:1 (t = trans), 14t-18:1, and 15t-18:1 isomers were resolved from the cis-18:1 isomers. The peaks of the 13t-18:1 and 14t-18:1 isomer pair, which always elute together, overlapped peaks of the 6c-18:1 (c = cis), 7c-18:1, and 8c-18:1 isomers; the peak of the 15t-18:1 isomer overlapped the major cis-18:1 peak, which was mainly due to 9c-18:1. Isothermal operations above or below 180 degrees C produced some additional overlapping problems. At 185 and 190 degrees C, the peaks of the 16t-18:1 and 13c-18:1 isomers overlapped. At 175 and 170 degrees C, the 16t-18:1 peak overlapped the 14c-18:1 peak, and the peaks of the 13t + 14t-18:1 isomer pair partially overlapped the major cis-18:1 peak. The separation of 11c-20:1 and alpha-linolenic acid and its geometric isomers was also affected by the column operating temperature. Isothermal operation of the SP-2560 column at 180 degrees C produced a baseline separation of 11c-20:1 and alpha-linolenic acid and its geometric isomers, whereas with the CP-Sil 88 column the best resolution was obtained at 170 degrees C. The results of this study show that the SP-2560 capillary column has a slight advantage over the CP-Sil 88 column for the simultaneous resolution of all the fatty acids generally found in partially hydrogenated vegetable oils.