The link between public health and migration control at the national level is well established in international migration research. This relationship is the starting point of our research on the Swedish management of refugees during the Second World War. The aim of the article has been to introduce the international research field migration and public health and analyze the role that public health strategies played in the organized refugee reception in the beginning of the 1940’s. We have studied the preparation and implementation of policies targeted to handle a larger amount of newly arrived refugees. Public health strategies played an important part in the preparations for the reception of a larger amount of refugees from Sweden’s neighboring countries. Existing laws and already established organizations created the frames for the emergence of organized refugee activities in the beginning of the 1940’s. This is very obvious in the routines that were established to identify and separate refugees that was suspected for having a contagious disease. In order to protect the national citizens all newly arrived had to pass through a health inspection. This included both a medical examination at the transit point as well as a two-week period in quarantine. After the quarantine the refugees were placed at permanent camps. The purpose of the isolation of the refugees was to prevent epidemics, most probably the isolation also contributed to perceptions about otherness of the newly arrived.