CASE STUDY Open Access Malaria control in South Sudan, 2006–2013: strategies, progress and challenges Harriet Pasquale 1 , Martina Jarvese 1 , Ahmed Julla 1 , Constantino Doggale 1 , Bakhit Sebit 1 , Mark Y Lual 1 , Samson P Baba 1 and Emmanuel Chanda 1,2* Abstract Background: South Sudan has borne the brunt of years of chronic warfare and probably has the highest malaria burden in sub-Saharan Africa. However, effective malaria control in post-conflict settings is hampered by a multiplicity of challenges. This manuscript reports on the strategies, progress and challenges of malaria control in South Sudan and serves as an example epitome for programmes operating in similar environments and provides a window for leveraging resources. Case description: To evaluate progress and challenges of the national malaria control programme an in-depth appraisal was undertaken according to the World Health Organization standard procedures for malaria programme performance review. Methodical analysis of published and unpublished documents on malaria control in South Sudan was conducted. To ensure completeness, findings of internal thematic desk assessments were triangulated in the field and updated by external review teams. Discussion and evaluation: South Sudan has strived to make progress in implementing the WHO recommended malaria control interventions as set out in the 2006–2013 National Malaria Strategic Plan. The country has faced enormous programmatic constraints including infrastructure, human and financial resource and a weak health system compounded by an increasing number of refugees, returnees and internally displaced people. The findings present a platform on which to tailor an evidence-based 2014–2018 national malaria strategic plan for the country and a unique opportunity for providing a model for countries in a post-conflict situation. Conclusions: The prospects for effective malaria control and elimination are huge in South Sudan. Nevertheless, strengthened coordination, infrastructure and human resource capacity, monitoring and evaluation are required. To achieve all this, allocation of adequate local funding would be critical. Keywords: Malaria control, Policy and strategy, Collaboration, Capacity building, Monitoring and evaluation Background In 2010, about 219 million malaria cases and 660,000 deaths were reported globally. The disease remains a major cause of morbidity and mortality, exacting its greatest toll in sub-Saharan Africa where over 80% of cases and 90% of deaths occur [1]. The huge burden could be ascribed to ef- ficient afro-tropical malaria vectors with strong vectorial capacities that maintain high levels of transmission. As well as, environmental factors and climatic changes, population movement, deteriorated socioeconomic situation, lack of access to effective anti-malaria treatment and use of fake anti-malarial drugs [2]. With increasing international fund- ing, malaria endemic countries have stepped up control ef- forts at individual and community levels [3]. Interventions include; early diagnosis with rapid diagnosis test (RDTs), treatment with artemisinin-based combination thera- py (ACT), indoor residual spraying (IRS), long-lasting insecticidal-nets (LLINs) and intermittent preventive treatment (IPTp) [1]. However, in post- conflict African environments, effective control has remained a daunting undertaking due to a multiplicity of challenges including high malaria transmission intensities. South Sudan has borne the brunt of years of chronic lib- eration warfare from the time of Sudan’ s independence * Correspondence: emmanuel_chanda@yahoo.co.uk 1 Ministry of Health, National Malaria Control Programme, Juba, Republic of South Sudan 2 Population Services International, Juba, Republic of South Sudan © 2013 Pasquale et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Pasquale et al. Malaria Journal 2013, 12:374 http://www.malariajournal.com/content/12/1/374