The present study aimed at comparing the trypanosome specific 18S-PCR-RFLP using samples stored either on Whatman filter papers (PCR-RFLP-fp) or in a commercial cell lysis and DNA protecting buffer (PCR-RFLP-pb) with the haematocrit centrifugation technique (HCT), a method widely used for the diagnosis of African Animal Trypanosomosis. Out of 411 head of cattle, 49 (11.92%) (CI=8.95-15.45) scored positive for the presence of trypanosomes by HCT whereas 75 (18.25%) (CI=14.63-22.33) and 124 (30.17%) (CI=25.77-34.86) scored positive using PCR-RFLP-fp and PCR-RFLP-pb, respectively. Out of the 49 positives by HCT, 14 (28.57%) (CI=16.58-43.26) and 28 (57.14%) (CI=42.21-71.18) were concordant by PCR-RFLP-fp and PCR-RFLP-pb, respectively. None of the PCR techniques detected parasites from the Trypanozoon group. Although HCT detected more cases of Trypanosoma vivax (33), species identification using PCR-RFLP-fp and PCR-RFLP-pb were significantly different (p<0.001) from the HCT technique. The use of DNA protective buffer is thus recommended as the output of the PCR-RFLP-pb is improved and the risk of contamination between samples is reduced.