Aims: Enterobacter sakazakii is an emerging food-borne pathogen that can cause rare but severe neonatal meningitis, bacteraemia and necrotizing enterocolitis. Contaminated powder infant formulae (PIF) have been identified as one of various infection routes. In this study, E. sakazakii was monitored in the processing environment of a PIF factory to identify possible dissemination routes. Methods and Results: The BOX-polymerase chain reaction (PCR), a fingerprinting technique which targets the repetitive BOX sequences, was used in routine to identify points of contamination and investigate clonal persistence. Two hundred E. sakazakii isolates were collected and typed. Most (70%) showed the same fingerprint that revealed the persistence of resident E. sakazakii strains in the processing environment. This method allowed to detect contamination of some PIF by dry-blending ingredients. Conclusions: Environment was the major cause for contamination of PIF and facilities. Some raw materials delivered as powder were also implicated. Significance and Impact of the Study: Routine BOX-PCR genotyping was very useful to trace and investigate in real-time dissemination of micro-organisms in the PIF plant and to implement a series of additional control measures to reduce the risk of final product contamination by E. sakazakii.