In this study, analyses were carried out to establish the impact of heating three species of fatty fish: trouts, herrings and sprats, on the lipids oxidation and on contents of eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids. The comminuted fish tissue was heated at restricted access of oxygen at temperature of 60, 100 and 160 °C for 15–120 min. Lipids, extracted with the Bligh-Dyer method, were determined for peroxide value (PV) and anisidine value (AV). The Fatty acid methyl esters were prepared directly from the tissue, whereas contents of EPA and DHA were determined with the GC/MS method. Depending on the temperature applied, 15-min heating of fish meat tissue caused 30–80% decrease of PN and 20–40% decrease of AV, on average. Generally, the continued heat treatment caused successive decreases in both PV and AV and the rate of this process was observed to increase along with an increasing temperature. The heating of trout and sprats at temperature of 60, 100 and 160 °C even for 1–2 h did not evoke losses either in EPA or in DHA content. In turn, in the case of herring caught during the pre-spawning season, ca. 90–120 min of heat treatment contributed to ca. 20–25% decrease in contents of these fatty acids.