BACKGROUND: Refugees and asylum seekers have high rates of risk factors for mental disorders. In recent years, Australia has experienced a rapid increase in asylum seeker arrivals, creating new challenges for services in areas with high settlement numbers. This paper describes the design, including analytic framework, of a project set in a refugee health service in the state of Victoria, Australia, as part of their response to meeting the mental health needs of their burgeoning local population of refugees and asylum seekers. In order to assist service planning, the primary aim of this study is to determine: 1) an overall estimate of the prevalence of psychiatric disorders; 2) the specific prevalence of post-traumatic stress disorder 3) the perceived need and unmet need for mental health treatment. The secondary aim of the study is to establish matched risk ratios based on an Australian-born matched comparison group from the 2007 National Survey of Mental Health and Well-Being. METHODS/DESIGN: A cross-sectional survey is used to estimate the prevalence of psychiatric disorders in refugees and asylum seekers attending a local refugee health service. Measures include the Kessler Psychological Distress Scale-10, the Post-Traumatic Stress Disorder-8, the General-practice User’s Perceived-need Inventory together with service utilisation questions from the National Survey of Mental Health and Well-Being. Data collected from refugees and asylum seekers (n = 130) is matched to existing data from Australian-born residents drawn from the 2007 National Survey of Mental Health and Well-Being (n = 520) to produce estimates of the risk ratio. DISCUSSION: The paper describes a prototype for what is possible within regular services seeking to plan for and deliver high quality mental health care to refugees and asylum seekers. A novel project output will be the development and dissemination of an epidemiological methodology to reliably compare mental health status in a relatively small target sample with a matched comparator group.