Cheeses are recognized as major dietary sources of CLA, a group of positional and geometric isomers of linoleic acid (18:2 cis9,cis12) with potential beneficial effects to human health. Bioactivity of CLA is isomer specific and is related to immune modulation, body fat reduction, and protection against atherosclerosis and cancer. Therefore, analytical methodologies to ensure accurate analysis of CLA contents and detailed distribution of positional and geometrical isomers are required. In this chapter we present an overview of the most useful chromatographical techniques, such as Ag+- HPLC and GC-MS. We present reported contents of CLA and the distribution of CLA isomers in cheeses obtained from milk of different ruminant species and using varied cheesemaking processes. These data is discussed, and we contrast the effects of cheese processing conditions, and the variation in cheese CLA resulting from milk fat composition. These factors in combination might explain at least part of the variation in contents of the fifteen CLA isomers identified in cheese. Concerning the effects of processing, heat treatments, ripening conditions and addition of starter cultures are candidates to explain the variation in CLA composition observed in cheeses. Conversely, milk fat composition might be affected by geographical origin, seasonality, and the animalsr diet, which appear to be the major determinant of CLA variation in cheeses. Finally, we discuss the contribution of cheeses for the habitual intake of CLA by population groups that is of concern considering the potential health benefits of CLA.