To determine the prevalence of common diseases in newly arrived refugee children, resettled in Sydney, by region of birth. To identify health needs of refugee children in Australia. We prospectively screened for common diseases in refugee children attending a specialist paediatric refugee clinic, the Children's Hospital, Westmead, between May 2005 and December 2006. Screening tests included full blood count, Mantoux, vitamin D level, hepatitis B serology, syphilis serology, Schistosomiasis serology and malarial antigens. There were 239 patients, the majority (75%) from Africa, with 127 girls and 112 boys. Thirty-six percent were 0-7 years old, 45% were 8-12 years old and 19% were 13-17 years old. Of those tested, 16% had Schistosomiasis, 5% had malaria and 4% were hepatitis B carriers. Of 216 children who had Mantoux tests, 33% were > or =10 mm and 24% were > or =15 mm, including four children with active disease (2 lymphadenitis, 1 pulmonary and 1 gastric). Vitamin D deficiency was the most common diagnosis: 61% had serum 25(OH)D3 <50 nmol/L. Anaemia was present in 15%. Disease prevalence was higher in children from Africa than Asia or the Middle East, and most of the children were asymptomatic. Given that we have only seen about 10% of the refugee children resettled in New South Wales, our results may not be generalisable to all refugees. Our findings suggest that screening refugee children for common treatable conditions, even if they are asymptomatic, is paramount. In addition to infectious diseases screening, nutritional deficiencies should routinely be screened for.