Forty individual patient sputum isolates of Burkholderia cepacia from two Australian cystic fibrosis (CF) centres more than 100 km apart were genotyped using pulsed-field gel electrophoresis (PFGE) with XbaI restriction enzyme digestion. Hospital 1 had an endemic strain with 19 of 20 isolates being closely related. This centre does not implement an inpatient segregation policy for its paediatric patients who constitute the majority of those colonized with B. cepacia. Hospital 2 did not have a single endemic strain; there were two different sibling clusters and a third cluster involving a cohabiting couple, but all other patients had unique isolates. One patient at Hospital 2 carried an organism closely related to the endemic strain from Hospital 1. Hospital 2 practises segregation of colonized inpatients and also segregation external to the hospital. It would appear that no nosocomial spread of infection is occurring with this policy.