Introduction: Diet is a complex set of exposures that frequently interact, and whose cumulative effects influence the results of health. This includes effects on systemic inflammation markers in metabolic disturbances and cardiovascular diseases. Various studies have been presented relating the effect of physical exercise on lipids, however, the results are still controversial. Objective: To describe fatty acid metabolism and the effect of physical exercise on secondary complications. Methods: An integrative review was conducted on topics in the Medline, Pubmed, Web of Science and Scopus databases, published up to the year 2017. Results: Fatty acids, depending on their biochemical characteristics and spatial configuration, have differentiated effect on cardiovascular health, however, studies still present contradictory results about the therapeutic use of certain fatty acids. Physical exercise appears to benefit fatty acid metabolism and attenuate the complications secondary to the intake of certain fatty acids, and potentializes the positive effects of distinct fatty acids. Conclusion: However, variants of physical exercise, such as intensity, duration, time of observation of effects of the results, limit the authors to concluding, with a certain degree of certainty, about the effect of physical exercise on fatty acids and secondary complications, since the studies in the literature continue to be contradictory.Keywords: fatty acids, exercise, inflammation, oxidative stress.