The current refugee crisis has forced European countries to face an increase in chronic disease and the re-emergence of previously eradicated infectious diseases. This study examines Eurostat statistics for the year 2015 for 28 European countries and Turkey to investigate the interplay of patterns of chronic and infectious diseases and migration integration indicators among European country groups. Study results indicate the prevalence of two distinct clusters of chronic and infectious diseases and migration integration indicators, whereby the group comprising major host countries such as Germany, Turkey, and Spain is contrasted with the second group comprising other countries. Country clusters differ in terms of all study variables (p < 0.0001). Increasing collaboration and developing measures to address health inequalities and improve refugee integration in order to reduce threats from chronic infectious diseases are advisable strategies for health policymakers in Europe.