Objective To assess the performances of Cobas 6000 e601 and EVOLIS BioRad in the detection of HIV, HBV and HCV in blood donors in Libreville (Gabon). Methods A cross-sectional investigation was conducted in July 2017 in a total of 2 000 blood donors recruited at the National Blood transfusion Center, Libreville Gabon. Among them, 363 donors were selected to compare the performances of COBAS 6000 e601 (electro-chemiluminescence) and EVOLIS BioRad in detecting HIV, HBV and HCV using Cohen's kappa coefficient. Results Both methods yielded similar results for the detection of HIV and HBsAg. A very good agreement of 93.39% and an excellent agreement of 98.90% were obtained for the detection of HIV and HbsAg, with kappa values of 0.80 and 0.98, respectively. The observed agreement of 91.86% was found for the detection of HCV, which gave a fair agreement between the two methods with kappa = 0.33. Conclusions The two evaluation methods showed a similar performance in the detection of HIV, HBV. However, given the high rate of intra and inter-genotypes recombination known for HIV and HBV, more robust techniques of detection such as polymerase chain reaction should be used to prevent post-transfusion contaminations.