Burkholderia cepacia is found in soils and waters, it can be used in biocontrol and bioremediation but is also a human pathogen. It is not yet clear what differentiates pathogenic from non-pathogenic strains of the organism. In this study the multiple replicon structure was investigated in 28 strains of B. cepacia by pulsed field gel electrophoresis. All strains examined, whether of clinical, environmental or plant pathogenic origin, were found to have two, three or four large (> 500 kbp) replicons. Many strains also contained small replicons. Clinical strains were more likely to have three or four large replicons than non-clinical strains. Multiple replicon structure was also demonstrated in B. gladioli and, Alcaligenes eutrophus.