Human African trypanosomiasis is a parasitic infection caused by protozoa belonging to Trypanosoma brucei subspecies. The clinical evolution of this disease is complex and might be because of the parasite itself, as genetic diversity has been observed in T. brucei ssp. We investigated the relationship between the genetic diversity of trypanosomes and the diversity of clinical patterns in Côte d'Ivoire. We studied clinical sleeping sickness cases, and genetically analysed the trypanosomes isolated from these patients. An important genetic monomorphism among stocks isolated in Côte d'Ivoire was observed by using various markers: isoenzymes electrophoresis, random amplified polymorphism DNA and PCR of microsatellite sequences. At the same time, the diversity of clinical patterns and evolutions was confirmed by clinical analysis. The existence of an individual susceptibility to disease (human trypanotolerance) should be taken into account even if our genetic conclusions might be distorted because the isolation success rates were particularly poor. In fact, we observed that the isolation success rate varied significantly depending both on the focus of origin (P=0.0002) and on the ethnic group (P=0.0317) of the patient. Further investigations are required in order to study a possible selective impact of the use of the kit for in vitro isolation of trypanosomes as an isolation technique.