Leishmaniasis, a parasitic disease transmitted by the sand fly, is almost always fatal if left untreated.
Many residents of southern Sudan are weakened by 19 years of war, while medical facilities are few and far between, making diseases even more dangerous than usual.
The Sudan Government and Sudan People's Liberation Army (SPLA) signed a truce two weeks ago but both sides have already accused each other of violating it.
The SPLA is fighting for more autonomy for the mainly Christian south from the Arabic-speaking, Muslim north.
Visceral leishmaniasis, also called Kala Azar, is endemic in parts of Sudan, Ethiopia and Somalia, but some MSF staff say that this year's outbreak is the worst they have ever seen.
"It is an overwhelming scene, with so many of the people coming to the clinic every day more dead than alive," said Dr Jose-Antonio Bastos, an MSF Operational Director who just returned from eastern Upper Nile State.
"The state of these patients is appalling. They are being carried on stretchers for days to make it to the clinic. They look pale and thin and are extremely anaemic."
Parasites
The MSF clinic in Lankien, eastern Upper Nile has received about 100 people suffering from leishmaniasis a week for the past six weeks.
Clinics in Malakal and Umm el Kher are treating more than 600 cases between them.
MSF officials point out that those who reach the clinics are the lucky ones who have not yet died.
"There is a clear overlap of those areas where Kala Azar is endemic and areas of conflict," said Dr. Bastos.
"Insecurity, malnutrition and poor access to health care lower the people's natural resistance to diseases and make for an environment where outbreaks like the current one occur."