Clinical consultation at Danila Dilba, an Aboriginal community-controlled health service in Darwin, were compared with consultations in Australian general practice. We described 583 consultations, using a questionnaire based on the International Classification of Primary Care. The methods were similar to those of the Australian Morbidity and Treatment Survey (AMTS) of consultations in Australian general practice undertaken by the University of Sydney Family Medicine Research Unit. Compared with Australian general practice consultations, consultations with Danila Dilba were more complex: more young patients, more new patients, more home visits, more problems managed, more new problems and more consultations leading to emergency hospital admission. Skin infections, diabetes mellitus, chronic alcohol abuse, rheumatic heart disease (or rheumatic fever) and chronic suppurative otitis media were much more commonly managed at study consultations at Danila Dilba than at consultations with general practitioners in the AMTS. Nearly all patients saw an Aboriginal health worker first, and nearly half the consultations were with Aboriginal health workers alone. The results suggest possible limitations of fee-for-item Medicare funding of Aboriginal community-controlled health services compared with existing block grant funding.