Fish farming has a long tradition in Central Europe. Aquaculture is highly developed here and even so, freshwater fish meat consumption is still very low. Freshwater fish meat is an important source of n–3 long-chain polyunsaturated fatty acids (PUFA), principally eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) which have an indisputable effect on human health and prevent the genesis of human coronary disease. Previous researches revealed many aspects affecting the PUFA quantity. In general, the fatty acid composition of fish lipids affects age, seasonal change, nutrition, sex, reproductive cycle, geographical location, etc. This review represents a step towards the characterization of the fatty acid composition of economically important freshwater fish species from different points of view, including the above-mentioned factors and taking into consideration the way of stunning and differences of lipid composition in individual fish body sections.