Despite the widely acknowledged health disparities between Indigenous and non-Indigenous Australians, little is known about consultations in primary care with Indigenous people. In particular, the nature of consultations in the Aboriginal Community Controlled Health Service (ACCHS) sector has been rarely studied. Data collection about consultations in primary care has been steadily improving, with good quality data now available on an ongoing basis about patient demographics, risk factors and consultation content in private general practice. This study aimed to characterise consultations at Townsville Aboriginal and Islander Health Service (TAIHS) in terms of patient demographics and consultation content. These could then be compared with existing datasets for local consultations in mainstream general practice and from a geographically distant ACCHS. We conducted a prospective questionnaire audit of all consultations at Townsville Aboriginal and Islander Health Service (TAIHS) over two fortnights, 6 months apart in 2000 and 2001. The questionnaire was adapted from one used in previous general practice surveys, and was completed by the treating clinician at the end of each consultation. The questionnaire described consultations using the following variables: date of consultation; patient age; ethnicity and gender; postcode and whether or not they were new to the practice; where they were seen; the provider of the service (doctor, nurse, health worker etc); Medicare level of consultation; patient reasons for encounter; problems managed; treatment and medications given; investigations; admissions; follow up; and referral. Proportions with 95% confidence intervals were calculated to facilitate comparisons with other datasets. Comparison was made with previously reported data from mainstream Townsville general practice (via the local BEACH study report) and from Darwin ACCHS (Danila Dilba). Of 1211 consultations studied, 1994 problems managed were recorded. TAIHS patients had a significantly younger age distribution than patients in mainstream general practice (as did patients at Danila Dilba). TAIHS consultations involved the management of more problems (1.65 problems per consultation; 95%CI [1.60, 1.70]), when compared with mainstream general practice (Townsville BEACH study 1.45 problems per consultation [1.37, 1.52]; 1.48 for Indigenous patients). Danila Dilba recorded an average of 1.58 problems managed per consultation (95% CI [1.51, 1.65]). The most frequently managed problems differed between all three datasets, and at TAIHS the most common problems managed were type 2 diabetes mellitus (11.3 times per 100 consultations), upper respiratory tract infections (9.6) and hypertension (7.9). Aboriginal Health Workers (AHW) saw the patient at TAIHS in 224/1213 (18.5%) of consultations, nurses (two Indigenous) participated in 513 (42.3%) of consultations, and a (non-Indigenous) medical officer saw the patient in 1070 (88.2%) of consultations. The Danila Dilba study found that 42.6% of their consultations involved an Aboriginal health worker only, and a health worker and a doctor managed 53.5%; only 3.9% were managed by a doctor alone without input from a health worker. The greater number of problems managed per consultation in ACCHS, compared with Indigenous patients in mainstream general practice, supports the assertion that ACCHS fill an important role in the health system by providing care for their largely Indigenous patients with complex care needs. The Medicare system as it was structured at the time did not encourage involvement of Indigenous health workers in provision of primary medical care. It remains to be seen whether introduction of the new enhanced primary care Medicare numbers will assist in this process. These findings have implications for ACCHS in other areas of the country and for other providers of primary health care for Indigenous Australians.