An outbreak of fatal septicaemia caused by Serratia odorifera biotype 1 involved infants at several hospitals; the common vehicle of infection was contaminated parenteral nutrition fluid. The transfusate had been made up in a flexible film isolator system. The implicated organism was recovered from surfaces inside the isolator, despite routine decontamination procedures having been carried out shortly before. Our investigation into the origin of contamination revealed several shortcomings in the infusate compounding process. We noted deficiencies in cleaning and decontamination procedures, and in storage and sterility testing policies, but the origin and mechanism of the contamination were unclear. Withdrawal of parenteral nutrition products and revision of decontamination procedures terminated the outbreak. The efficacy of peracetic acid treatment of flexible film isolators, given the circumstances of this outbreak, may need further investigation. Regular training and assessment of admixture technicians is important.