This paper evaluates adherence with secondary preventative treatment and follow up of acute rheumatic fever (ARF) within the Katherine region of the Northern Territory after the introduction of an ARF register. We aimed to assess the rate of adherence with penicillin prophylaxis and follow-up guidelines in patients with previous ARF and the effect of factors such as age, sex, disease severity and clinic attendance. Retrospective study. Five Indigenous Community Health Centres located in the Katherine region of the Northern Territory, Australia. Fifty-nine people resident in five communities who were prescribed monthly prophylactic penicillin for ARF during the 24 months between September 2002 and September 2004. All subjects were Indigenous. Main outcome measures were the number of penicillin injections received over the 24-month period and frequency of echocardiogram and specialist follow up in comparison to Rheumatic Fever Registry Guidelines. Mean adherence with prophylaxis was 56% of prescribed doses. A non-significant trend towards improved adherence was seen in children, patients with less severe disease and those who attended the clinic more frequently. Rheumatic Fever Registry Guidelines for echocardiogram and specialist review were met by 63% and 59% of subjects, respectively. Within this population adherence with penicillin prophylaxis is inadequate to protect against recurrence of ARF and consequent worsening of rheumatic heart disease. In addition, the Rheumatic Fever Registry Guidelines for specialist follow up and echocardiogram are not being adhered to for many patients.