The stability of vitamins A, E and C, and the iron and selenium content were determined in two types of long chain-polyunsaturated fatty acid (LC-PUFA) supplemented milk-based powdered infant formulas (IF), during an 18-month storage period at 25 and 40 °C. The first type (IF-A) was supplemented with vitamin A as retinol acetate. The second type (IF-B) was supplemented with vitamin A as retinol palmitate. Both types were also supplemented with vitamin E as α-tocopherol acetate and with vitamin C as ascorbic acid. The two formulas studied had higher vitamin A (140% and 139%), vitamin E (109% and 198%) and vitamin C (167% and 118%), but lower iron (65.0% and 65.3%) and selenium (72.9% and 79.4%) than the amounts declared on the label. As expected, all the studied vitamins showed decreases during storage, and these decreases were higher in formulas stored at 40 °C. The losses of vitamin A at 40 °C after 18 months of storage were 27.5% in IF-A and 29% in IF-B, while vitamin E losses under the same conditions were 23.1% and 28.1%, and vitamin C losses under the same conditions were 28.4% and 48.6%. All these losses justify the over-fortification of the aforementioned vitamins in these LC-PUFA supplemented IFs. Iron and selenium content remained unchanged throughout storage.