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Four Trypanosoma (T.) congolense reference clones with known isometamidium sensitivity and 16 T. congolense stocks from cattle in Kénédougou in south-western Burkina Faso, an area with known history of drug resistance, were characterised with the standard mouse test (SMT) and the drug incubation infectivity test (DIIT). All field stocks from Kénédougou were resistant to 1.0 mg/kg bw isometamidium in the SMT. Fourteen stocks (87.5%) also proved to be refractory to 10 mg/kg bw. Testing with the DIIT confirmed the results of the SMT. By comparison to reference clones, all the Kénédougou populations expressed high levels of resistance to isometamidium.