ABSTRACT: OBJECTIVE: To document the prevalence of nutritional deficiencies, infectious diseases and susceptibility to vaccine preventable diseases in Karen refugees in Australia. DESIGN: Retrospective audit of pathology results. SETTING: Community based cohort in Melbourne over the period July 2006-October 2009. PARTICIPANTS: 1136 Karen refugee children and adults, representing almost complete local area settlement and 48% of total Victorian Karen humanitarian intake for the time period. MAIN OUTCOME MEASURES: Prevalence of positive test results for refugee health screening, with breakdown by age group (<6 years, 6-11 years, 12-17 years, 18 years and older). RESULTS: Overall prevalence figures were: anaemia 9.2%, microcytosis 19.1%, iron deficiency 13.1%, low vitamin B(12) 1.5%, low folate 1.5%, abnormal thyroid function tests 4.4%, vitamin D<50 nmol/L 33.3%, hypocalcaemia 7.4%, raised alkaline phosphatase 5.2%, abnormal liver transaminases 16.1%, hepatitis B surface antigen positive 9.7%, hepatitis B surface antibody positive 49.5%, isolated hepatitis B core antibody positive 9.0%, hepatitis C positive 1.9%, eosinophilia 14.4%, Schistosoma infection 7%, Strongyloides infection 20.8%, malaria 0.2%, faecal parasites 43.4%. Quantiferon-gold screening was positive in 20.9%. No cases of syphilis or HIV were identified. Serological immunity to vaccine preventable diseases was 87.1% for measles, 95% for mumps and 66.4% for rubella; 56.9% of those tested had seroimmunity to all three. CONCLUSIONS: Karen refugees have high rates of nutritional deficiencies and infectious diseases and may be susceptible to vaccine preventable diseases. These data support the need for post-arrival health screening and accessible, funded catch-up immunisation.