Background In August 2010, Pakistan experienced floods that affected 20 million people in 78 districts, killed 1800, damaged or destroyed about 2 million homes, 514 health facilities and inundated a land mass the size of England. (1) Prior to this current crisis, Pakistan already had about four million internally displaced people and refugees due to the war along the Afghan border and the 2005 earthquake in Khyber-Pakhtunkhwa (formerly North-West Frontier Province). Health indicators in Pakistan were dismal even before the floods, with maternal mortality at 230 (190-280) per 100 000 live births and under-5 mortality at 89 per 1000 live births. (2) Most of the flooded populations comprise the lowest socioeconomic quintiles that were already facing neglect. This crisis has worsened their plight. Relief agencies Relief operations were mainly carried out by the Pakistani government, the army and international agencies such as the World Health Organization (WHO), the United Nations Children's Fund (UNICEF), Medecins Sans Frontieres and the United States Agency for International Development (USAID). (3) In addition, civilian volunteers, independent teams of physicians, nongovernmental organizations and various other groups with little experience in disaster relief were also working in the field. The Pakistan army provided the most visible rescue operations but was overextended with massive rescue efforts, shoring up and breaching dykes, as well as fighting the war in the tribal areas. The National Disaster Management Authority was established after the earthquake in 2005. However, it does not have a dedicated post for an individual overseeing the public health aspect of the disaster. Widespread mistrust of governmental agencies, primarily stemming from perceived corruption and mismanagement, has hindered donors and citizens from cooperating with governmental initiatives. We strongly recommend that the government take the lead in coordinating the public health response and allocate personnel and resources to that effect. Infectious diseases Between August and September 2010, 6.2 million consultations for gastroenteritis, respiratory infections, malaria and dermatologic conditions were reported to WHO from 50 of 64 affected districts, with countless more predicted to fall sick in the period that followed. (1) Using surveillance data from flood-affected districts, WHO reported mounting cases of Crimean-Congo haemorrhagic fever, dengue fever, cholera, falciparum malaria, measles and polio. (3) A nationwide diphtheria outbreak was also unfolding at the time of writing this paper. An oral cholera vaccine is available and recommended for use in humanitarian emergencies by WHO (4) yet it has not been recommended for use in flood-affected areas due to perceived logistic difficulties in delivery, e.g. two-dose regimen, vaccine production capacity. While such obstacles were overcome for delivery of the H1N1 pandemic flu vaccine, mass cholera vaccination was not given priority in Pakistan. With the manufacture and potential availability of a cheap and effective cholera vaccine from India, mass vaccination may have been a consideration for the affected populations in Pakistan. Adverse impact on polio eradication has been significant. Pakistan is one of only four countries where polio remains endemic. Eradication remains a challenge due to the complex situation exacerbated by the war in Afghanistan, insurgency in Pakistan and the resulting mass movement of people. By 9 November 2010, Pakistan accounted for about 62% (111 cases) of all 180 polio cases from endemic countries, (5) and most new cases were from flood-affected areas. (3) However, WHO increased efforts at delivering vaccination services in 45 flood-affected districts and, due to enhanced cooperation between the Pakistan Expanded Program on Immunization (EPI), WHO and UNICEF, national immunization days went ahead as planned. …