There are concerns in Australia about inadequate rates of childhood immunisation, an important preventive measure to reduce infectious diseases. The population passing through the Melbourne Juvenile Justice Centre (MJJC) comes from a background at high risk for inadequate immunisation and outbreaks can occur in residential institutions. MJJC residents were invited to participate in a study by completing a medical officer-administered risk behaviour questionnaire and/or giving a blood sample. Ninety residents completed the questionnaire; 83 gave blood samples. Sera were tested for measles, mumps, rubella and hepatitis A, B and C markers using standard commercial assays. Diphtheria and tetanus were tested with an ELISA in a public health laboratory familiar in the technique. Sixty four per cent (53/83) of participants were non-immune to at least one component of MMR and 44.6% (37/83) non-immune to either tetanus or diphtheria. Despite 61.1% of participants reporting injecting drug use, only 28.2% had protective levels of anti-HBs, 6.1% were positive for anti-HBc (2.4% equivocal), 22.9% were anti-HCV positive and 9.6% had markers of exposure to hepatitis A virus. These results show suboptimal levels of immunity in this institutional setting with the potential for disease outbreaks. Many residents miss adolescent school-based programs for immunisation because of truancy and early school leaving. Despite considerable risk of blood-borne viruses, many MJJC residents are inadequately vaccinated against hepatitis B.