INTRODUCTION This study aimed to assess self-reported screening practice in the antenatal setting, factors associated with screening, barriers to universal testing for HIV and follow-up for infants born to hepatitis C virus (HCV)-infected women. METHODS A total of 3100 general practitioners (GPs) were mailed the survey. The half from Victoria was randomised to receive their questionnaire by registered post or regular post. All GPs from New South Wales (NSW) received their questionnaire via regular post. RESULTS The overall response rate was 70%. Registered post resulted in a higher cumulative response rate compared with regular post (86% vs. 67%P < 0.001). Greater than 90% of respondents always screened for syphilis, rubella and hepatitis B virus. Testing for HIV and HCV approached 66% in NSW. In Victoria more respondents always screen for HCV (72%) compared with HIV-1 (64%). Respondents from NSW were less likely to screen for toxoplasmosis (adjusted odds ratio (AOR) 0.64 (0.43, 0.94) P = 0.02) or HCV (AOR 0.75 (0.61, 0.92) P = 0.005) compared with Victoria. Older respondents were more likely to screen for toxoplasmosis (AOR 1.54 (1.05, 2.27) P = 0.03), cytomegalovirus (OR 1.5 (1.0, 2.1) P = 0.05) and chlamydia (AOR 1.88 (1.27, 2.77) P = 0.002). Of respondents who have managed a pregnant woman with HCV 25% inappropriately test infants for infection before one month of age. CONCLUSION This study highlights the need for more education and resources to increase HIV testing rates and to improve follow-up of an HCV-exposed infant.