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The artisanal fish preservation methods in Uganda are characterized by extreme operating conditions. Consequently, vital nutritional components diminish in value and quantity which renders fish consumer nutritionally insecure. To establish the magnitude of nutritional loss, duplicate samples of Mukene Rastrineobola argentea were collected from Kiyindi landing site on L. Victoria and Moone landing site on L. Kyoga. Each set of duplicate samples was divided into five portions and kept on ice. For each preservation method a portion was processed into respective products at Food Bioscience and Agri-Business Laboratories aside from the control (fresh) sample. Both preserved and control samples were analysed for nutrient loss at Department of Chemistry, Makerere University using AOAC methods. The composition of fatty acids was determined by methanolysis gas chromatography and Mass spectrophotometry of the resultant methyl esters. The results indicate that nutrients of all preserved samples did not vary significantly from the control except for some fatty acids. The Eicosapentaenoic acid (EPA) in fresh samples declined from 6.72% to 1.08% in deep-fried samples constituting 83.93% nutrient loss. The sum ratio ω3:ω6 as well as EPA: DHA (Docosahexaenoic) ratio in fried samples also varied significantly (p<0.5) lower than 0.668 and 0.20 for the average of either preservation methods and experts recommended ratio respectively. Further research has been recommended to ascertain the causative factor, since Mukene frying is being promoted in the Great lakes region as alternative method to sun-drying. In conclusion, regular consumers of fried Mukene do not benefit much from the nutritional and health attributes of Omega 3 and 6.