The influence of feed supplemented with dietary sources of n-3 polyunsaturated fatty acids (PUFAs), namely flaxseed and algae Schizochytrium sp., on the fatty acid composition of lipids from Japanese quail eggs was studied. Two groups of quails were fed for 19 weeks, starting from 6th week of life. Lipid fractions from dried egg mass of total of 4300 eggs of control and experimental group were analysed. The fatty acid profile was affected in both triacylglycerols and phospholipids. The significant (P < 0.05) increase in n-3 PUFAs up to 7.33% in the total lipids, α-linolenic acid (ALA, 18:3) up to 4.57% in triacylglycerols, docosahexaenoic acid (22:6, DHA) up to 23.91% in phosphatidylethanolamine and up to 4.35% in phosphatidylcholine as well as the significant (P < 0.05) reduction in n-6/n-3 ratio in the lipid fractions to the range of 0.9–3.7 was observed in experimental group. The incorporation of different n-3 into lipids was selective: ALA was found in the triacylglycerol fraction, whereas EPA, DPA and DHA were detected in the phospholipid fractions, exclusively at sn-2 position. The studies showed that the feeding quails with modified diets is effective way of biofortifying the eggs with nutritionally desired n-3 PUFAs.