Background The Medicare-rebated Health Assessment for Aboriginal and Torres Strait Islander People (Medicare Benefits Schedule [MBS] item number 715) has been progressively implemented across Australia since 1999. Objectives This paper explores some of the reasons why the uptake of Health Assessment for Aboriginal and Torres Strait Islander People remains low in some metropolitan general practices. Methods Semi-structured interviews and self-complete mail surveys with 31 general practice staff and practitioners were combined with an audit of practice systems and patient medical records in seven general practices in Sydney. Results Barriers to MBS item number 715 uptake included low rates of Indigenous status identification, lack of knowledge of MBS item numbers, lack of organisational teamwork within the practice and avoidance of billing specific MBS item numbers. Discussion The low uptake of MBS item number 715 in some metropolitan areas is of particular concern given the known gaps in Aboriginal and Torres Strait Islander health. Targeted action is required to address the barriers to uptake and re-evaluate the use of MBS item number 715 as a key performance indicator.