Abstract Background Populations in Europe are becoming increasingly ethnically diverse, and health risks differ between ethnic groups. The aim of the HELIUS (HEalthy LIfe in an Urban Setting) study is to unravel the mechanisms underlying the impact of ethnicity on communicable and non-communicable diseases. Methods/design HELIUS is a large-scale prospective cohort study being carried out in Amsterdam, the Netherlands. The sample is made up of Amsterdam residents of Surinamese (with Afro-Caribbean Surinamese and South Asian-Surinamese as the main ethnic groups), Turkish, Moroccan, Ghanaian, and ethnic Dutch origin. HELIUS focuses on three disease categories: cardiovascular disease (including diabetes), mental health (depressive disorders and substance use disorders), and infectious diseases. The explanatory mechanisms being studied include genetic profile, culture, migration history, ethnic identity, socio-economic factors and discrimination. These might affect disease risks through specific risk factors including health-related behaviour and living and working conditions. Every five years, participants complete a standardized questionnaire and undergo a medical examination. Biological samples are obtained for diagnostic tests and storage. Participants’ data are linked to morbidity and mortality registries. The aim is to recruit a minimum of 5,000 respondents per ethnic group, to a total of 30,000 participants. Discussion This paper describes the rationale, conceptual framework, and design and methods of the HELIUS study. HELIUS will contribute to an understanding of inequalities in health between ethnic groups and the mechanisms that link ethnicity to health in Europe.