Previous research with the Australian Morbidity and Treatment Survey (1990-1991) showed significant differences in general practitioner characteristics and patient mix of male and female GPs. Even after adjusting for these, it was seen that male and female GPs managed different types of medical conditions. The proportion of female GPs increased from 19.6% in 1990-1991 to 37.1% in 2009-2010. This study investigates whether differences remain two decades later. Analysis of 2009-2010 Bettering the Evaluation and Care of Health (BEACH) data examining GP characteristics, patient encounter characteristics, patient reasons for encounter (RFE), problem types managed and management methods used, by GP sex. Whether GP sex was an independent predictor of problem types being managed, or management methods used, was tested using multiple logistic regressions and Poisson regression. 988 GPs recorded 98 800 GP-patient encounters. Adjusted differences in clinical activity of male and female GPs. After adjustment, compared with male GPs, females recorded more RFEs about general and unspecified issues and endocrine, female genital, pregnancy and family planning problems; and fewer concerning the musculoskeletal, respiratory, skin and male genital systems. Female GPs managed more general and unspecified, digestive, circulatory, psychological, endocrine, female genital and social problems; recorded nearly 20% more clinical treatments and referrals; recorded nearly 10% more imaging and pathology tests; and 4.3% fewer medications. After two decades, even with increased numbers of female GPs, the differences in problems managed by male and female GPs remain, and will probably continue. Female GPs use more resources per encounter, but may not use more resources in terms of annual patient care.