Conjugated linoleic acid (CLA) is a naturally occurring micronutrient in milk fat and dairy products consisting of a group of geometric and positional isomers. The purpose of this study was to assess the level and type of CLA isomers found in two commercial processed cheeses (portions and slices) as well as to monitor their evolution during the different manufacturing stages. Total CLA concentrations ranged from 7.5 to 7.9 mg/g of fat, and rumenic acid (cis-9,trans-11 C18:2), the isomer responsible for the biological functions, represented >80% of total CLA. trans-11,cis-13 and trans-11,trans-13 were, with approximately 4% each, the second main CLA isomers. trans-trans isomers accounted for <10% of total CLA. The processing parameters used in this research had negligible effects on the CLA content of processed cheese and did not modify the isomer profile in these dairy products, thereby confirming the stability of rumenic acid during manufacturing.