The emergence of type 6B Streptococcus pneumoniae resistant to five antibiotics (penicillin, chloramphenicol, trimethoprim–sulphamethoxazole, erythromycin and tetracycline) in both the Northern Territory and Queensland prompted an investigation of the genetic relatedness and patterns of migration of the isolates. Pulsed field gel electrophoresis of genomic DNA of 74 multiple drug-resistant (MDR) isolates cultured in both regions between August 1988 and June 1997 showed that 100% of MDR isolates from the Northern Territory and 96% of MDR strains from Queensland were genetically indistinguishable or closely related to the index strain. None of a further 65 type 6B isolates that were resistant to one or two, or susceptible to all of the above antibiotics, were clonally related to the MDR pneumococci. The geographical distribution of the MDR type 6B clone increased over time. The index strain, first isolated in Darwin in August 1988, was identified in Brisbane, 2900km distant, less than 4 years later and subsequently in other Queensland centres. Surveillance programmes are important to monitor the emergence and spread of potentially invasive MDR pneumococcal clones in countries that are well serviced by air and road transport.