Descriptive epidemiological studies can point towards health problems specific to migrants and minorities. To investigate etiological associations and for public health planning, analytical epidemiological studies are required. In Germany, epidemiological studies rarely include migrants and minorities. Underlying reasons are the high mobility and socio-cultural diversity of these groups. In addition, a classification by ethnic or national categories is problematic. This review discusses problems and possible solutions in the planning and design of analytical epidemiological studies among migrants and minorities.