AbstractGeneral practice has been the subject of extensive reforms over the 1990s in Australia as elsewhere. Reforms have attempted to improve quality and contain the overall cost of health care, and have often been seen as reducing the autonomy of medical professionals. This paper examines the impact of financial constraints and incentives introduced during the 1990s on Australian GPs' perceptions of autonomy. An existing seven component definition of autonomy and six themes that emerged from reviewing publications were used to construct focus group questions. A total of 25 GPs participated in four focus groups. Those who participated believe that their financial autonomy has been diminished by policy changes and consumer expectations. They also perceive that their ability to control clinical decisions, which they regard as the most important aspect of professional autonomy, has been reduced along with financial autonomy. Organized medicine in Australia sees financial accountability and clinical decision making as polar opposites, and has continued to argue that fee‐for‐service payment is the only appropriate method of remuneration, despite increasing evidence that this does not guarantee clinical autonomy. Major changes to the financing of general practice in Australia are required to address the concerns of GPs, governments and patients. Copyright © 2003 John Wiley & Sons, Ltd.