Infectious diseases are responsible for about one quarter of all deaths worldwide and it is likely that major epidemics will emerge in the near future. Through the airline system, diseases can spread around the world rapidly and are more and more likely to do so. At the same time, air connectivity is essential for countries with inadequate land-based infrastructure, in particular during an epidemic when incoming humanitarian assistance is essential. This illustrates the trade-off of passenger airline operations during an epidemic: the likelihood of further spreading of the disease versus the role in combatting that same disease. Policies that prevent infectious diseases from spreading are in place, but knowledge of their effectiveness and impact on the passenger logistics is limited.