Aquaculture industry has sustained its development on the use of products obtained from marine fish species. Main industrial products in this field are both the flour and fish oil, which have a high nutritional and economic value. Fish oil has been found to be a scarce raw material, which has a high content of polyunsaturated fatty acids (PUFA n-3) and has been classified as a functional food because of the benefits they bring on the consumer’s health. Paradoxically, high PUFA n-3 content makes the fish oil highly susceptible to the autooxidation processes that lead to the transformation of PUFA N-3 in peroxides, aldehydes, ketones and polymers that are responsible for oxidative cell damage. In this document we explore the processes in which primary and secondary products are generated through oxidation, and the protection mechanisms against oxidative damage and the negative effect of primary and secondary products of lipid autoxidation on nutritional quality of balanced feeds, fish health and quality of meat products for human consumption.