BACKGROUND In the past decade, a large influx of migrants presented in Europe. Their country of origin was mainly either Syria or Eritrea. Public health institutions in host countries in Europe are challenged to screen and care for migrant populations with regard to infectious diseases. METHODS We performed a systematic literature review (according to PRISMA guidelines) to define the infectious disease profile of migrants originating in Syria and Eritrea. RESULTS The search resulted in 825 papers of possible relevance for infectious diseases in migrants from Syria, of which, after screening, we included 35 in the systematic review. A further 265 papers of possible relevance for infectious diseases in Eritrean migrants were screened, of which we included 27 in the systematic review. In migrants from Syria, leishmaniasis was the most frequently reported infectious disease. In addition, colonisation with drug resistant, Gram-negativ bacteria was reported. In the Eritrean migrants the infectious disease most described in the selected papers was louse-borne relapsing fever. Other frequently reported infectious diseases were scabies and Plasmodium vivax malaria. CONCLUSION Our systematic analysis defines the profiles of infectious diseases for migrants from Syria and Eritrea and serves as an evidence base for public health screening and care of presenting migrants.