Background: There is extensive and varied interaction between the pharmaceutical industry and the medical profession. Most empirical research concerns contact between individual physicians and industry, and reflects North American experience. We sought to clarify the extent and nature of relationships between the pharmaceutical industry and Australian medical organizations. Methods: We administered questionnaires to 63 medical organizations concerned with clinical practice, continuing medical education or professional accreditation, or the political representation of medical professionals. Results: Survey instruments were received from 29 organizations, giving a response rate of 46%. Seventeen of these organizations (59%) had received support from one or more pharmaceutical company in the past financial year. Support was predominantly for annual conferences, with some support for continuing medical education, research, travel and library purchases. The majority of organizations had an academic journal or newsletter, and 10 (34%) accepted revenue from pharmaceutical advertising. Twenty organizations (72%) had policies or guidelines covering their relationship with industry. Few organizations indicated that they would be unable to continue their activities without pharmaceutical industry support. Conclusion: These data indicate a high level of interaction between the pharmaceutical industry and medical organizations in Australia. While most organizations have policies for guiding their relationship with industry, it is unclear whether these are effective in preventing conflicts of interest and maintaining public trust.