Introduction: Nine cases of Bacillus cereus bacteremia occurred in five neonatal intensive care units (NICUs) of the Assistance publique-Hôpitaux de Paris (AP-HP) between August and December 2016. Method: The investigation into these cases included a review of medical records to identify a common source, environmental sampling (surfaces, equipment, batches of pasteurized milk, parenteral nutrition), a genetic comparison of clinical and environmental strains, a retrospective survey of AP-HP microbiology laboratories to estimate the incidence of B. cereus bacteremia in NICUs, and finally an evaluation of the milk supply chain, from production to administration. Results: The retrospective survey showed that the incidence of B. cereus bacteremia in the NICU had increased from 0.05 to 0.33 per 100 admissions between 2014–2015 and 2016. The only common factor among all cases was that they had received a lipid emulsion from the same manufacturer, as did the majority of newborns in the NICU. No common source contaminated with B. cereus was identified. B. cereus was isolated from batches of pasteurized breast milk (two batches consumed by two of the cases and others not delivered) and a few environmental samples. Comparison of the strains revealed significant genotypic diversity. Improvements were implemented following an evaluation of the milk distribution system. Conclusion: In late 2016, an increase in the number of cases of B. cereus bacteremia was observed in five neonatal intensive care units (NICUs) of the AP-HP. The involvement of contamination in batches of pasteurized milk was not proven. No common source could be identified.