Interest has been increasing to enhance the contents of healthy polyunsaturated fatty acid (PUFA) in milk. However, trans fatty acids and conjugated linoleic acid (CLA) can be altered after thermal processing and high pressures disrupt the milk fat globule membrane, exposing the lipid core and helping its oxidation. The objective of the present research was to study whether processing can alter the fatty acid composition of milk and if these changes are affected by PUFA concentration as previous studies suggest. Two cow milk batches (500 L each), one naturally enriched in PUFA, were processed to obtain pasteurized; high temperature, short time; UHT; high pressure; and microwave pasteurized samples. The detailed fatty acid composition was analyzed with special attention to trans fatty acids and CLA isomers. Results showed that after high temperature, short time processing, total CLA content increased in both milk batches, whereas sterilization resulted in a sigmatropic rearrangement of C18:2 cis-9,trans-11 to C18:2 trans-9,trans-11. The extent of these effects was greater in milks naturally enriched in PUFA.