The aim of this study is to compare the prevalence of chronic disease risk factors in humanitarian arrivals to Sydney, New South Wales (NSW) with the Australian Indigenous and non-Indigenous populations aged 35–44 years. Data on risk factors collected from 237 refugees presenting to the NSW Refugee Health Service (RHS) from January 2015 to August 2016 were retrospectively analysed and compared with data from the Australian Health Surveys, 2011–13 for the Indigenous and non-Indigenous Australian populations. This study found significantly higher levels of triglycerides (z=3; 95% CI, 0.16–0.26); hypertension (z=3.2; 95% CI, 0.17–0.29); and smoking (z=3.5; 95% CI, 0.27–0.33) in refugees compared with the general Australian population. The Indigenous population had significantly higher levels of triglycerides (z=4; 95% CI, 0.16–0.26); body mass indexes (BMIs) (z=3.3; 95% CI 0.58–0.72); and smoking (z=5.4; 95 CI 0.27–0.33) compared with refugees. Based on the study findings, screening for chronic disease risk factors from age 35 years may be warranted in all humanitarian arrivals to Australia, along with dietary and lifestyle advice.