The lipid status of Atlantic salmon (Salmo salar L.) embryos has been compared between embryos developing in incubator nests installed in the natural environment (UmbaRiver, Kola Peninsula) and those developing in a laboratory (in aquaria). The developmental stage of eye pigmentation selected for comparison is characterized by the highest sensitivity of the embryos to environmental factors. The content of certain classes of total lipids and fatty acids was different between the two groups of embryos, and the ratios between the relative content values for some of the compounds were different as well. The difference may be due to environmental factors (temperature, oxygen levels, running water in the nests, etc.) affecting the developing embryos, and they may determine the subsequent embryonic and postembryonic development of the fish.