The presence of aflatoxin M1 (AFM1) in infant formula and aflatoxin B1 (AFB1) in cereal-based foods for infants marketed in Kosovo was investigated. One hundred and forty-three samples collected during 2016-2017 were analysed by ELISA and suspected positive samples were further analysed by LC-MS/MS. A positive incidence of 15.0% for AFM1 in baby milk and 62.14% for AFB1 in infant cereal-derived samples was found. According to the Commission Regulation and Kosovo Codex Regulation, the AFM1 levels in baby milk samples reached the interval of 0.008 to 0.123 µg kg^-1, with two samples that exceeded the maximum residue levels (MRL). The AFB1 detected levels, in cereal-based foods for infant samples, ranged from 0.008 to 0.116 µg kg^-1, with one of them exceeding the MRL. This survey indicates that the risk of exposure to this population group through diet is evident in Kosovo. A food safety alert system and surveillance program are essential for ensuring infant health and the entire population.