Changing migration dynamics in the Mediterranean Sea and differences in infectious diseases (ID) burden between the countries of origin have raised questions whether public health actions are needed to avoid the transmission of ID. Screening newly arrived migrants for ID is one health monitoring option, offering opportunities for prevention, early detection and treatment. The authors conducted a survey among country experts in non-European Union countries of the Mediterranean and Black Sea, in order to explore current ID screening practices and policies for newly arrived migrants. The association between the existence of guidelines and the proportion of refugees in the population was also estimated. Eighteen country experts responded (90%) out of the 20 invited. Eleven countries (61%) implemented screening programmes and six (38%) had national guidelines. Screening was performed most often for tuberculosis at the holding level. A higher proportion of refugees in the population was associated with the existence of guidelines for screening (p = 0.05). Fourteen experts (88%) considered screening among migrants useful. The results show that screening for ID in newly arrived migrants is relevant for non-EU countries of the Mediterranean and Black Sea. Common guidelines could be promoted focusing on both individual and public health benefits of screening programmes.