ω3-polyunsaturated fatty acids (PUFA) are known to have several beneficial effects, such as preventing the occurrence of cardiovascular events in adults and improving the development of the central nervous system during fetal life and childhood. Dairy products enriched in PUFA are now available on the market and can help consumers to meet the ω3-PUFA daily intake recommendations. Although PUFA are prone to oxidation, little information exists regarding the alterations they undergo when products containing PUFA are stored. In this study, five infant formulae (IF) and five ω3-PUFA enriched Ultra High Temperature (UHT)-milk products were examined during storage at room temperature in terms of fatty acid (FA) composition and trans fatty acid (tFA) content until the end of shelf life by chromatography techniques. The IF included two follow-on formulae, two first-age formulae and a special medical purpose formula with different fat contents (from 2.6% to 27.7%). In the ω3-PUFA enriched UHT-milk products the milk fat was replaced by eicosapentanoic fatty acid (EPA) and docosahexaenoic acid (DHA) rich oils. The fatty acid content of all samples remained stable whereas some variations were observed for the tFA isomer content (p < 0.05) in the UHT-milk samples.