Bacillus cereus, a ubiquitous human foodborne pathogen, can persist in different environment, including dry conditions. In this study, we explored the genetic diversity of B. cereus isolates from infant milk formulas. Out of 83 samples, B. cereus was confirmed in 26 (31.3%). Isolates were resistant to penicillin G and ampicillin (100%), trimethoprim‐sulfamethoxazole (84.6%), and erythromycin (3.8%). Ent, hbl, and cer genes were detected in 21 (80.8%), 2 (7.7%), and 11 (42.3%) isolates, respectively. Randomly amplified polymorphic DNA (RAPD) analysis, using set of three primers, provided an overall genetic distance of 95% between B. cereus isolates. A group of seven emetic strains and another two enterotoxic strains were indistinguishable by RAPD, revealing their high clonality. In conclusion, we detected a high proportion of pathogenic B. cereus isolates in infant milk formulas. The majority of isolates harboring both cer and ent genes showed high clonality, pointing food processing environment as probable contamination source.Practical applicationsDetection of Bacillus cereus in powdered infant milk formulas, the prevalence of emetic and diarrhegenic genes, and especially the simultaneous presence of both types of genes in the same isolate, confirm the importance of B. cereus as foodborne pathogen. The consumption of contaminated formula may cause serious health problems in babies, which emphasizes the need to improve B. cereus monitoring and characterization. The clonal relationship between strains, revealed by RAPD analysis, may point to the source of infection and the corresponding prevention measures to improve food safety. Moreover, the identical RAPD profile of cer positive strains obtained with AG15 primer enables the application of this analysis in screening for emetic B. cereus isolates.