Fish are the most important source of n-3 highly unsaturated fatty acids (HUFA) in the human diet and, with declining wild stocks, an increasing proportion is being provided by aquaculture. Paradoxically, aquaculture fish diets have traditionally incorporated fish oil and meal derived from wild fisheries. Continued aquaculture development requires fish oil to be replaced with vegetable oils, the only sustainable alternative. However, vegetable oils lack n-3 HUFA and so flesh from fish reared on these diets can also have reduced n-3 HUFA and thus reduced nutritional quality. This accepted, the flesh n-3 HUFA content should be an economically important trait, however to be included in the breeding goal the trait must be measurable. In the present study, we investigated whether the flesh n-3 HUFA content of salmon can be estimated in a non-fatal way. We showed that a general regression model based on flesh lipid content, morphometric and blood fatty acid measurements could estimate and predict flesh n-3 HUFA content. This would allow a choice from a range of selection methods, including mass selection or within-family selection, if this important flesh quality trait is to be included in future salmon breeding programmes.