OBJECTIVE: To determine the prevalence and clonality of non-toxigenic Corynebacterium diphtheriae biovar gravis in a community with two cases of endocarditis caused by this organism. SETTING: A Koorie (Aboriginal) community in Gippsland, eastern Victoria, in 1994. METHODS: Nose and throat swabs were collected from 359 community contacts of the cases and cultured for C. diphtheriae. Strains isolated from the contacts were compared by pulsed-field gel electrophoresis (after digestion with Sma1, Not1 and Sfi1) with those from the invasive cases in the same community, another invasive case in Victoria, a cluster of invasive cases in New South Wales (NSW) (1990-1991), and other stored strains isolated from skin ulcers and sore throats. RESULTS: Non-toxigenic strains of C. diphtheriae biovar gravis were isolated from throat swabs of five of the case contacts. Uniform DNA patterns were found for the two community cases, the other Victorian case, nine of ten isolates from NSW, and the five throat isolates from case contacts. CONCLUSION: An invasive clone of C. diphtheriae biovar gravis appears to have been responsible for the three Victorian cases of endocarditis. It was also present among case contacts and responsible for previous invasive cases in NSW. Prophylactic treatment should be considered for clearly defined contacts in all instances where C. diphtheriae is isolated from a normally sterile site, regardless of the toxigenic nature of the strain.