South Sudan: Country in Crisis

Find out more about cholera, the deadly diarrhoeal disease we are currently responding to in South Sudan

South Sudan Crisis

The conflict that erupted on 15th December 2013 in South Sudan has led to the destruction of medical and other civilian structures. More than a million people are displaced within the country, with another 200,000 seeking refuge in countries bordering South Sudan.

The fighting rendered many of the existing health facilities non-functional with no medical supplies or human resources to offer as medical staff fled for their lives, leaving populations without access to health facilities or anyone to respond to their basic needs. 

During the conflict, Médecins Sans Frontières/Doctors Without Borders (MSF) has had to relocate services to pre-existing facilities which have become overstretched. We have built tented hospitals, worked under temporary shelters and set up inflatable hospitals. With over 3,500 local and international staff working in the country, we have set up emergency projects to respond to the growing needs of people directly affected by the crisis.

Central Equatoria, Jonglei, Upper Nile and Unity states are the most affected areas in South Sudan since the fighting started. As a result, we increased our operations in these states by starting new emergency projects and providing non-food items - such as mosquito nets and blankets - as well as water and sanitation support. Our teams are also carrying out outreach activities, assessments and monitoring people’s health needs across the country.

  • We currently run more than 22 projects in nine of South Sudan's 10 states.
  • Since 15th December 2013 we have carried out 330,679 consultations (41 percent of which were for children under five), admitted 14,601 patients into our hospitals (of whom 57 percent were children under five), treated 2,951 war wounded and carried out 2,538 surgeries. We have also delivered 8,320 children
  • We currently have more than 3,500 international and local MSF staff working in the country. In addition, 76 expatriates provide support to MSF's operations in South Sudan from neighbouring countries (such as EthiopiaKenya and Uganda).

Read the full crisis update

South Sudan crisis map, June 2014

Latest news in-depth:

A girl with burns to her head is treated in the MSF clinic set up at the camp for displaced people in the grounds of the United Nations Mission to South Sudan base in Juba.

Our work before independence

In early 2005, a peace agreement was signed between North and South Sudan. This agreement ended a prolonged civil war of more than 20 years.

In January 2011 South Sudan decided, after a referendum, to secede from the North. This led to the formal independence of the Republic of South Sudan on 9th July 2011.

Despite this, Africa’s newest country is still facing a humanitarian crisis. Diseases, malnutrition and displacement are rife. The health system is extremely weak and under resourced and many regions are still facing ongoing violence.

Background: 2012

This is an extract from our latest Activity Report, looking back on our work in the previous year.

The massive influx of refugees into South Sudan caused Médecins Sans Frontières/Doctors Without Borders (MSF) to launch one of its biggest emergency programmes of 2012.

Conflict in Sudan’s Blue Nile and South Kordofan states led to the arrival of thousands of refugees in Unity state and Upper Nile state during the first half of the year.

Maban refugee crisis

But the land is inhospitable: in the dry season water is scarce and the baked clay is extremely hard to drill, while in the rainy season it is a flood plain and only accessible by air. There is virtually no scope for agriculture or grazing animals.

In Maban county, Upper Nile state, an estimated 110,000 refugees in four camps became entirely dependent on humanitarian organisations. However, their response failed to meet refugees’ basic needs, and in some camps mortality levels had reached double the emergency threshold by July.

MSF called for more humanitarian assistance as teams ran three field hospitals and seven outreach clinics across the camps, carrying out up to 8,000 medical consultations per week and caring for people suffering from the effects of lack of food and water and long journeys on foot.

Staff provided treatment for malnutrition, skin and respiratory infections and diarrhoea. MSF also addressed the issue of water supply, managing boreholes and hand pumps.

A team worked in Yida refugee camp in Unity state, where the population quadrupled to 60,000 people between January and July. MSF offered inpatient and outpatient care, and operated four feeding centres.

By September, death rates had been brought under the emergency threshold. However, the camps were soon faced with an outbreak of hepatitis E – a potentially fatal virus transmitted through contaminated water.

The refugees remain entirely dependent on humanitarian assistance.

Violence and displacement in Jonglei state

Brutal intercommunal clashes continued to cause widespread displacement in Jonglei. People escaped deep into the bush, only to become vulnerable to malaria, diarrhoea and respiratory diseases.

In central Jonglei, MSF runs a hospital in Pibor town and two outreach clinics in the villages of Lekwongole and Gumuruk. The repercussions of an exceptionally bloody attack on Lekwongole and Pibor in December 2011, in which hundreds of men, women and children were killed or wounded and two MSF medical facilities were damaged and looted, persisted into 2012. People were coming from the bush weeks after the attack, seeking treatment for badly infected wounds.

Further attacks resulted in severe damage to MSF facilities in Lekwongole and Gumuruk in August and September. Again, tens of thousands of people fled and staff ran a makeshift clinic in the bush to provide basic and emergency healthcare.

In total, MSF carried out more than 32,000 medical consultations across the three facilities in 2012. The resurgence of a rebel militia in this part of Jonglei state led to an increased military presence and almost daily clashes in the area by the end of the year.

In northern Jonglei, MSF runs a hospital in Lankien and an outreach clinic in Yuai. After Pieri village was burned down, the residents never returned. MSF therefore handed over the clinic, focusing instead on mobile medical assistance.

Staff carried out 100,000 consultations and also treated 30,000 patients for malaria and 1,000 patients for kala azar (visceral leishmaniasis) during outbreaks in 2012.


A region contested by Sudan and South Sudan, Abyei is prone to conflict and population displacement. MSF runs a hospital in Agok, 40 kilometres south of Abyei, providing a wide range of services, including reproductive healthcare and treatment for severe malnutrition, as well as a tuberculosis (TB) ward and emergency surgery.

In April, casualties from an air raid in Abiemnom in Unity state were brought to Agok hospital, where staff carried out lifesaving surgery. MSF also distributed relief items to people displaced by the attack, vaccinated children and conducted medical consultations.

A team ran mobile clinics in nine locations that are only accessible during the dry season. In November, they began mobile medical activities for the nomadic Misseriya population in the northern Abyei area. This was the first time MSF had been able to reach the area since July 2010.

The Abyei teams conducted a total of 29,200 consultations, helped deliver 860 babies and treated more than 3,500 children for malnutrition.

MSF water and sanitation expert Erik Heyer at a water point in Doro refugee camp in Maban county, South Sudan

Basic and specialist health services

In Unity state capital Bentiu, MSF runs a feeding programme. Staff also supported the hospital personnel to treat people wounded in cross-border fighting. Towards the end of the year, the team started to offer TB care so that patients do not have to travel to the programme in Leer for treatment.

In 2012, the number of cases of kala azar in Unity state was far higher than in recent years: 740 patients with the disease were treated by MSF at Leer hospital. The team also treated 5,200 people for malnutrition, enrolled 630 patients on TB treatment, and provided support for TB care at the clinic in Koch.

In Nasir, Upper Nile state, MSF runs a hospital providing a full range of medical services, including surgery. The team regularly responded to violent trauma incurred during cattle raids and tribal clashes.

At Yambio hospital, Western Equatoria state, MSF offers paediatric, outpatient, inpatient and maternity services. Staff carried out more than 23,100 consultations and treated 13,970 children for malaria.

Ten health posts were supported with staff training and drug supplies. When the area was hit by flooding, the Yambio team distributed relief kits to over 1,000 families.

In Northern Bahr El Ghazal, MSF runs the 250-bed Aweil civil hospital, focusing on maternal healthcare and paediatrics, including malnutrition. From July to December, MSF mobile clinics responded to a malaria outbreak and treated nearly 12,000 people.

The paediatric mortality rate in the hospital decreased from 20 per cent at the beginning of 2009 to 5 percent by the end of 2012.

A small MSF hospital in Gogrial town, Warrap state, provides basic healthcare and emergency surgery. In 2012 staff carried out 37,000 outpatient consultations and launched emergency responses to a measles outbreak and a spike in malnutrition.

In December, 47 women received fistula repair surgery. Obstetric fistulas are injuries to the birth canal most often caused by prolonged or obstructed labour. They cause pain and incontinence, which can lead to social stigma.

Malaria response in Lakes state

In Lakes state, MSF launched a malaria response from October to December in Rumbek town, Rumbek North, Ciubeit and Yirol. Teams supported health facilities by donating 30,000 rapid diagnostic tests and providing 20,000 mosquito nets and medicine to treat 7,350 patients.

At the end of 2012, MSF had 2,415 staff in South Sudan. MSF has been working in the area that is now South Sudan since 1983.

Patient story

Priscilla* was among the first wave of refugees to arrive in Maban county from Sudan.

There is hunger here because there is not enough food. It’s even worse if children are sick because they are malnourished. There is water, but just not enough for all these people. Surviving in this camp is not easy.

We fled the first fighting, still in the rainy season. Along the way, we were moving, but we could not race. It took us over two weeks to escape. We drank water from rivers. Many people got sick along the way, especially from malaria. As we fled, we passed through villages that were half empty. Some had already left, but others came with us when they saw us running.

Once we arrived at the border crossing-point, we felt safe. We stayed there two or three weeks. For the first time, people started to feel the pains they had not felt so far because they were so concentrated on running and saving their lives.

*The patient’s name has been changed.


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