Background - France has long been a country of immigration and in some respects may be seen to have a generous policy with respect to asylum seekers and access to health care for migrants. The French state notably provides healthcare access for undocumented migrants, through state medical aid and since 1998 has had a humanitarian policy for granting temporary residence permits for medical reason (TRPMR) to migrants. Within a context of political debate, reform and tightening immigration control we will examine this latter policy focusing especially on the dilemmas that arise for physicians of migrant patients when they are requested to write medical certificates as part of a TRPMR application. In a 2017 reform the key role of making recommendations on the granting or not of permits was handed over to Ministry of the Interior health inspectors. Recommendations are made after perusal of medical certificates established by the migrant’s physician and complementary evidence. Main body The writing of medical certificates by a physician would seem straightforward. This is far from the case since it raises a number of ethical dilemmas. These occur within a physician-patient relationship embedded within a social contract between the State, the physician and the migrant patient. To clarify the ethical issues arising 3 vignettes based on practice within an infectious disease unit at a large Paris hospital have been developed. The vignettes highlight ethical dilemmas in the care for migrants with tuberculosis (dilemma in defining health and disease), chronic hepatitis (dilemma between beneficence and do not harm), and HIV / AIDS (issue of deservingness). We will go on to reflect on issues of social justice and responsibility for the health of migrants within a globalized world. Conclusions - Criteria for residence permit delivery appear less than clear-cut and are interpreted in a restrictive way. Neither are the consequences of refusing a residence permit taken into account. We call for an empirical transnational ethics study involving countries implementing similar TRPMR policies. We also call for inclusion of lobbying competences into the medical undergraduate curricula, in order to breed future generations of physicians skilled in defending social justice.