BACKGROUND An outbreak of Burkholderia cepacia septicaemia occurred in our neonatal unit over a 9-week period in 2001, affecting 23 babies and two died. A second outbreak lasting 8 days occurred a year later, affecting five babies. METHODS Neonatal Intensive Care Unit, Kuala Terengganu Hospital. OBJECTIVE To review the patient characteristics and the risk factors for septicaemia in the first outbreak. METHODS Retrospective review of records and in the first outbreak a case-control analysis with 23 matched controls for risk factors for septicaemia. RESULTS In the first outbreak, median birthweight was 1670 g (range 860-3760) and median gestational age was 32 weeks (range 27-41). There were 32 episodes of septicaemia, and five and two patients had two and three episodes, respectively. The mortality rate was 6.3% per septicaemic episode. Multiple logistic regression showed the presence of a prior long line was associated with first septicaemic episode (OR 7.07, 95% CI 1.37-36.47 with P = 0.019) but not prior assisted ventilation. The organism was isolated from the water of an oxygen humidifier in the delivery room, three ventilator water traps and one humidifier water trap in the neonatal unit. In the second outbreak, six episodes of septicaemia occurred in five neonates with median birthweight 2060 g and median gestational age 32.5 weeks. The organism was isolated from two ventilator water traps. CONCLUSIONS These two outbreaks of Burkholderia cepacia subsided with general infection control measures. The sources of these two outbreaks were not identified.