This study examined the prevalence of the intestinal spirochaetes Brachyspira aalborgi and Brachyspira pilosicoli in different Western Australian (WA) populations. Faecal samples included 287 from rural patients with gastrointestinal symptoms, comprising 142 from non-Aboriginal and 145 from Aboriginal people; 227 from recent healthy migrants to WA from developing countries; and 90 from healthy non-Aboriginal individuals living in Perth, WA. DNA was extracted from faeces, and subjected to PCR assays for both species. B. pilosicoli-positive individuals were confined to the rural Aboriginal (14·5%) and migrant (15·0%) groups. B. aalborgi was detected at a lower but similar prevalence in all four groups: rural non-Aboriginals, 5·6%; rural Aboriginals, 6·9%; migrants, 7·9%; controls, 5·6%. In migrants and Aborigines, the presence of B. pilosicoli and B. aalborgi was associated (P<0·001), suggesting that colonization by B. pilosicoli may be facilitated by colonization with B. aalborgi. Amongst the Aboriginal patients, logistic regression identified both spirochaete species as being associated with chronic diarrhoea, failure to thrive and being underweight. Both species may have pathogenic potential, but B. aalborgi appears more host-adapted than the opportunistic B. pilosicoli.