Data on differences by ethnicity in cardiovascular diseases (CVDs) and diabetes, reflecting the influence of diverse cultural, social and religious factors, are important to providing clues to disease aetiology and directing public health interventions and health care resources. Methods: Through a network of European public health researchers and searches of bibliographic databases and internet sites, we determined the availability and characteristics of ethnically relevant data on mortality and morbidity from coronary heart disease (CHD), stroke and diabetes, in current European Union countries; data from the four countries comprising the UK were assessed separately. Results: In total, 25 countries had one or more relevant data sets (72 in total); however, two-thirds (n = 47) of the data sources came from only eight Nordic and Western European countries. For several countries, no data could be identified. Ethnically relevant, national death registers were available in 24 countries. Country of birth was the most common indicator of ethnicity. Data on CHD, stroke and diabetes morbidity among migrant and ethnic minority populations are currently scarce; both between and within countries, there are important differences in how ethnicity as well as disease outcomes are defined and measured which limits data comparability. Conclusion: Reliable routine data are key to evidence-based public health policies at both national and EU level. EU countries have a relatively weak base for assessing needs and planning health care interventions for its migrant and ethnic minority populations. The lack of ethnically relevant data on CVD and diabetes across the EU needs to be addressed urgently.