The profile of polyunsaturated fatty acids in cheeses obtained through fermentation by lactic acid bacteria Lactobacillus helveticus and Streptococcus thermophilus were evaluated. The milk used to make the cheeses came from cows fed with flaxseed oil and annato. The cheeses presented microbiological and physic-chemical quality with in the standards established by the legislation for Staphylococci and Listeria. With maturation, there was a reduction in the coliform values for both treatments. Regarding the counts of lactic acid bacteria, these remained viable until the 30th day of maturation and the proteolytic bacteria decreased. For antioxidant capacity, the treatment containing the combination of the strains obtained high ABTS values. There was no significant difference between the treatments with respect to the color of the samples. For texture, there was a significant difference for the parameters cohesion and elasticity. No increase in CLA content was observed in the form of its two main isomers, however, the levels of polyunsaturated fatty acids were increased.