He worked as a general practitioner from 1974-1975 in Bougaa (Algeria). After his specialisation in internal medicine he worked from 1985-1988 in the Democratic of Congo as coordinator of the clinical studies on HIV/AIDS of "Projet SIDA" in Kinshasa. He is one of the first physicians who studied and described the clinical manifestations of HIV infection in Africa. He was a member of the international team that investigated and controlled two haemorrhagic fever outbreaks in the Democratic Republic of the Congo (Ebola in Kikwit 1996 and Marburg in Durba, 1999). In 2004-2005 he worked at the Infectious Diseases Institute in Kampala (Uganda) to assist with the roll out of antiretroviral therapy. He was involved in research projects concerning the management of HIV and HIV co-infections in Uganda, the Central African Region, Ethiopia and South Africa.
Since 2013 prof. Colebunders has been involved in research concerning the aetiology of Nodding syndrome (NS) and onchocerciasis-associated epilepsy (OAE). In 2015 prof. Colebunders obtained an ERC Advanced Grant for a transdisciplinary study to identify the cause of NS and ways to decrease the incidence of OAE. This study (NSETHIO), is performing epidemiological, entomological, parasitological, virological and metagenomic studies concerning OAE in Tanzania, Uganda, South Sudan, DRC and Cameroon.