In this study, the effect of pasteurisation temperature on fatty acid composition of cheese was investigated. The fatty acid composition of raw and different heat-treated milk, salt and salt-free cheese were determined using cheese made from raw milk at temperatures varying between 70 and 90°C for 5min. Generally, C16:0 palmitic acid was the major fatty acid present in all milk and cheese samples. C18:1 t11 vaccenic acid was the major trans fatty acid (TFA) in all samples. C18:2 cis-9, trans-11 (Rumenic acid) was the major CLA isomer in these samples. Pasteurisation temperatures had no effect on TFA, CLA and fatty acid composition of the milk and cheese samples. © 2011 Society of Dairy Technology.