Biological, social and behavioural factors influence doctors to prescribe different types of medications to male and female patients. Secondary analysis of data from the Australian Morbidity and Treatment Survey 1990-1991 was conducted using multiple logistic regression to discriminate male and female patient encounters in general practice. The approach used considered possible confounding influences of GP and patient characteristics. The results showed that females were significantly more likely than males to receive prescriptions for: antibiotics; hormones; drugs affecting the central nervous, cardiovascular and urogenital systems; drugs for allergy and immune disorders; ear and nose topical preparations, and skin preparations, even after taking into account morbidity differences. If males and females were treated according to their presenting problems, differences in morbidity patterns would account for the management differences. However, the present investigation would suggest that GP and patient behaviours are also important factors that lead to differences in the prescriptions received by male and female patients in general practice.