Although peace has been restored to most of Uganda, attacks carried out by the Lord's Resistance Army in the north, and by the Allied Defence Forces in the southwest, are ongoing and have resulted in major population displacements.

From the 1999 MSF Activity Report:

MSF has run a programme to combat the tropical disease trypanosomiasis. This disease, also known as sleeping sickness is passed by infected Tse Tse flies and is characterised by fever, wasting and sluggishness.

MSF's programmes run in Omugo in the Northeastern district of Arua, and in Moyo and Adjumani in the extreme north of Uganda.

MSF screens for the disease and provides treatment. Currently, MSF and its collaborators are trying to identify the causes of resistance to treatment and through the MSF campaign to push for access to medicines, MSF hopes to ensure a reliable future supply of efficient medicine.

MSF teams regularly bring assistance to the displaced in the highly insecure Bundibugyo district. In April 1999, MSF provided emergency assistance to 15,000 newly displaced in Bundibugyo town including a mass vaccination campaign against measles. The team also set up water points and supplied drinking water to the displaced sites. Unfortunately, insecurity forced MSF to evacuate after several weeks.

MSF also runs an integrated health programme close to the Kenyan border in Moroto district.. There has been a great deal of ethnic violence in this area over recent years which has led to population displacement and a deterioration of the health services. MSF's objective is to improve the general health status of the semi-nomadic Pokot ethnic group, through a sustainable and integrated health system.

MSF is rehabilitating and upgrading the Amudat Health Centre. Since the project started in 1997, clean drinking water has been made available at the Health Centre, a new tuberculosis (TB) ward has been built. There are also 70 hospital beds, one-third of which are occupied by people suffering from Kala Azar.