Previous research has found that female injecting drug users (IDU) are younger and more likely to be involved in risky behaviours such as needle sharing and sex work than male IDU. Aboriginal female drug users, in particular, are over-represented in IDU and prison populations. These factors place female IDU at increased risk of health problems and complicate issues such as homelessness, unemployment and poverty. Although a substantial body of research exists, little trend analysis has been done in Australia and much of the previous literature has focused on treatment populations. Cross-sectional data from 1996 to 2003 from regular IDU in Sydney interviewed as part of Australia's drug monitoring system, the Illicit Drug Reporting System (IDRS) were examined for trends over time. The demographic characteristics, drug use patterns and self-reported risk behaviours of the most recent sample (2003) were analysed for gender differences. Female IDU were younger in all sample years. Female IDU were more likely to identify as Aboriginal or Torres Strait Islander (ATSI) and engage in sex work. There has been a steady increase in these proportions over time. Female IDU were less likely to have a prison history, although there has been an increase among both male and female IDU over time. There were no gender differences in drug use patterns or frequency of drug use. Larger proportions of females report lending needles. Reports of lending and borrowing needles have decreased over time among both male and female IDU. Female IDU may place themselves at greater risk than male IDU by being more likely to share injecting equipment and engage in sex work. Treatment and other measures to reduce harm may need to be targeted specifically at women and, in particular, indigenous women.