OBJECTIVE To compare the standard microscopic examination, the polymerase chain reaction (PCR), and the immunochromatography test (ICT) to determine the best method for screening blood donors for malaria parasites in Sudan. METHODS A total of 100 blood donors were screened for malaria parasites by standard microscopic technique, ICT, and PCR Blood films were examined microscopically using standard Giemsa staining techniques. Qurum (Canadian Company) malaria kits were used to perform the ICT. For performing PCR, DNA was extracted using Chelex method and amplified by the moderately repetitive DNA sequence pBRK-l. RESULTS Using PCR, a total of 21 blood samples were positive; 8 (38%) of them showed negative blood films and 7 (33%) were negative on ICT. Four blood samples that tested positive by ICT despite a negative PCR and microscopic examination were proved to be false positives. The false negativity of both the microscopic examination and ICT was found to be significant. The sensitivity of microscopy was 61.9% and of ICT was 66.7%, while the specificity of microscopy was 100% and of ICT was 94.9%. When direct microscopy was considered as the standard technique the sensitivity of ICT was 100% and the specificity was 94.3%. CONCLUSIONS Although PCR is more sensitive and more specific, it is unaffordable. Microscopy for malaria when compared to ICT showed similar sensitivity at low cost. However, all human plasmodium species can be detected using the microscopy while only two species (P. falciparum and P. vivax) can be detected by ICT. The detected false positivity of ICT is not inconsequential since this implies the rejection of a greater proportion of blood donations. Therefore, microscopy is considered more suitable for screening Sudanese blood donors for malaria parasites prior to donation at the present time. CONCLUSIONS To establish a reference malaria diagnosis unit in each blood bank in Sudan as well as to train blood bankers to perform microscopic examinations.