Significant progress has been made in controlling human African trypanosomiasis (HAT) caused by T.b. gambiense as evidenced by the clear decline in the number of reported cases in recent years. Now the prevailing discourse is about the possible elimination of HAT and the need to integrate treatment for it into existing health structures. However, “Hot spots” still exist and one of which is the northeastern region of Orientale Province in the Democratic Republic of Congo (DRC). In this region there is neither a monitoring system nor working health centres capable of diagnosing and treating patients. An assessment carried out by the DRC’s national program to fight HAT and Doctors Without Borders/Médecins Sans Frontières (MSF) in 2004 discovered an alarming prevalence (2.1%) in the region. Between June 2007 and March 2009 MSF launched a HAT monitoring program in the Doruma, Ango, and Bili health zones. The overall prevalence was found to be 3.4%. Of the 46,601 people tested (18,559 through passive screening and 28,042 through active screening), 1,570 people were infected with T.b. gambiense. Of that group, 947 (60%) were in the first phase of HAT, indicating intense transmission of the disease. Due to the acute insecurity in this region of the DRC, MSF had to suspend its projects in March 2009, even though the limits of the disease foci had not yet been reached. Moreover, the disease could spread further by the displacement of entire populations who are fleeing the insecurity and heading for areas that had been previously “cleaned” of HAT. The intervention, which took place during a crisis situation, leads us to question the feasibility of eliminating HAT and integrating treatment in crisis areas where health services are at a minimum.