Background/Objectives: To determine the impact of a not hydrolyzed fermented infant formula containing heat-killed Bifidobacterium breve C50 and Streptococcus thermophilus 065 (HKBBST) on the incidence of allergy-like events during the first 2 years of life in children at high risk of atopy. Subjects/Methods: This multicenter, randomized, double-blind, controlled study included infants at high risk of atopy. Infants used HKBBST or a standard infant formula (SIF) since birth until 1 year of age, and were followed at 4, 12 and 24 months after birth. Skin prick tests (SPTs) for six foods and six aeroallergens were systematically performed and adverse events (AEs) were recorded. In case of potentially allergic AE (PAAE), allergy could be further tested by SPT, patch tests and quantification of specific IgEs. If cow's milk allergy (CMA) was suspected, an oral challenge could also be performed. Results: The study included 129 children, 63 were randomized to SIF, 66 to HKBBST. The use of HKBBST milk did not alter the proportion of CMA but decreased the proportion of positive SPT to cow's milk (1.7 vs 12.5%, P ¼ 0.03), and the incidence of digestive (39 vs 63%, P ¼ 0.01) and respiratory potentially allergic AEs (7 vs 21%, P ¼ 0.03) at 12 months, and that of respiratory PAAEs at 24 months (13 vs 35%, P ¼ 0.01). Conclusions: HKBBST decreased the incidence of PAAEs in children with family history of atopy, during the first months of life and after the formula was stopped. Oral tolerance to cow's milk in infants at high risk of atopy may therefore be improved using not hydrolyzed fermented formulae.