OBJECTIVES: To explore how Australian general practitioners use pharmaceutical decision-support (PDS) systems; to determine GPs' perceptions of the deficiencies and strengths of these systems; and how they believe they can be improved. DESIGN AND SETTING: Qualitative analysis of discussion from three focus groups of GPs (from one rural and two urban Divisions of General Practice) between April and May 2002. PARTICIPANTS: 22 GPs selected to include users of the five most popular prescribing/clinical practice software products available in Australia. MAIN OUTCOME MEASURES: Advantages and disadvantages of using PDS software; ideas for improving PDS systems; attitudes to electronic evidence-based guidelines. RESULTS: GPs believed that important interactions may be missed because of desensitisation resulting from too many alerts (which also intrude on workflow); that interaction alerts need to be severity graded and only significant ones should appear; and that improved computer-user interface design could enhance the usefulness of PDS systems. CONCLUSIONS: Our results will provide useful feedback to government, software vendors and software developers on the needs and expectations of end users and on the development of agreed software standards.