Yellow fever is an acute vaccine preventable viral haemorrhagic disease found mainly in tropical regions of Africa and America. It is caused by a Flavivirus which is transmitted by mosquito bites and has a natural reservoir in non-human primates. The virus is endemic in tropical areas of Africa and Latin America, with a combined population of over 900 million people . The “yellow” in the name refers to the jaundice that affects some patients. Approximately 200,000 cases and 30,000 deaths occur annually especially in Africa  where the case-fatality rate ranges from 15–50% . The yellow fever virus can cause devastating epidemics of potentially fatal, hemorrhagic disease. The disease can be confirmed through, serological testing by way of ELISA for yellow fever virus-specific IgM or isolation of the virus from blood samples. These are the recommended standard diagnostic tests for yellow fever although PCR tests which detect the viral genetic material have been used [1, 4]. The number of yellow fever cases has increased over the past two decades due to declining population immunity to infection, deforestation, urbanization, population movements and climate change. This disease has no cure and treatment is symptomatic, aiming at reducing symptoms for the comfort of the patient and mass vaccination is the most important preventive measure . Immunization of people at risk interrupts human to human transmission of the yellow fever virus especially when adequate vaccination coverage levels are reached. The vaccine is safe, affordable and highly effective, and appears to provide protection for 30–35 years or more . The vaccine provides effective immunity within one week for 95% of persons vaccinated [6, 7]. Despite mass vaccination campaigns to prevent and control these outbreaks, the risk of major yellow fever epidemics, especially in densely populated, poor urban settings, both in Africa and South America, has greatly increased . Consequently, yellow fever is considered an emerging, or reemerging disease of considerable importance.
In December 2010, the Ugandan Ministry of Health (MOH) declared a Yellow fever outbreak based on nine laboratory confirmed samples from the five districts of Abim, Agago, Kitgum, Pader and Lamwo in northern Uganda. This part of Uganda, home to game reserves and national parks, borders South Sudan and Kenya where previous cases of yellow fever have been reported [9, 10]. This was the largest ever recorded yellow fever outbreak in the country with an overall attack rate of 13 cases per 100,000 population based on confirmed cases . A cumulative total of 181 confirmed cases with 45 deaths (CFR = 24.8%) were recorded, with no new cases reported since February 2011 [4, 11]. The CFR among males (29.6%; 32/108) was nearly twice that of females (17.8%; 13/73) and the ages of suspected yellow fever cases varied from 3 months to 83 years with a mean age of 28.2 years and a standard deviation of 17.5 years . Previous yellow fever outbreaks in Uganda had fewer or single cases [12, 13]. For about 40 years now, no yellow fever cases had been reported in Uganda [14, 15]. However, larger outbreaks had been reported in East Africa, with attack rates (cases per 100,000 persons) of 6,800 in Sudan  and 27.4 in Kenya . In addition, the yellow fever vaccine is not part of the Expanded Program for Immunization (EPI) vaccines given routinely especially to children under five. It is mainly people travelling abroad from Uganda that are required to receive the yellow fever vaccine.
The Ugandan Ministry of Health developed a national response plan prioritizing surveillance and laboratory confirmation, case management, social mobilization and health education, and reactive vaccination to contain the outbreak. The national response team included Ministry of Health of Uganda, World Health Organization (WHO), Uganda Red Cross society (URCS), United Nations International Children Emergency Fund (UNICEF), and the U.S. Centers for Disease Control and Prevention (CDC). Others were African Field Epidemiology Network (AFENET), RESPOND (Responding to emerging pandemics and threats), MSF-Holland, Uganda National Expanded Program on Immunization (UNEPI) and World Vision. This campaign was conducted between the 22nd and 26th of January 2011 and targeted all persons aged 6 months and above in the affected districts. Approximately one million people were targeted in the affected region.
Pader district is found in northern Uganda and this region borders South Sudan which is prone to sporadic yellow fever outbreaks . In this district, residents lead a primarily agricultural lifestyle, growing crops and raising cattle, sheep, and poultry. Community settlements near bushes and forests are common since most people have just returned from internally displaced peoples camps after the war in northern Uganda. They venture into the forests mainly for hunting and harvesting bamboo for sale. Potential mosquito-breeding sites include baobab trees with tree holes, rock holes, and a water reservoir on the outskirts of villages. The district has a projected population of 205,898  and the yellow fever attack rate was 2.9 cases per 100 000 population with females being more affected than males.
During the response, 177 vaccination posts were created, 354 health workers and 590 volunteers from 295 villages were identified and trained. Vaccination posts were mainly health facilities (both public and private not for profit), outreach sites for routine EPI vaccines and a few schools. During the campaigns, Uganda Red Cross society (URCS) supported community-based activities such as social mobilization, transportation of vaccines and provision of logistics. The URCS volunteers also supported organization of beneficiaries, issuing of vaccination cards and other support activities at the various vaccination posts in this district. The target population for vaccination in this campaign was all persons aged 6 months and above with a target vaccination coverage of at least 80%. After the campaign, the reported or administrative yellow fever vaccination coverage was 75.9% and this was below the targeted 80% . Administrative yellow fever vaccination coverages in the other districts were: Abim 120.5%, Agago 81.6%, Kitgum 77.6% and Lamwo 73.9% . When the target coverage is not reached, the potential for an epidemic increases since there is a low prevalence of neutralizing antibodies to the yellow fever virus from previous vaccination or naturally acquired infection.
Underreporting of vaccine doses administered usually results in underestimation of the coverage. It is important to conduct coverage surveys to validate reported administrative coverages so as to inform imminent (mop-up activities) and future immunizations strategies. Probability-based surveys such as cluster surveys can estimate vaccination coverage even if the size of the target population is not known [19, 20]. The aim of this survey was to estimate yellow fever vaccination coverage in Pader district and determine the reasons for non vaccination to recommend possible mop-up actions, guide future vaccination efforts and contribute to the control of yellow fever in the country.