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Introduction: In Nigeria, microscopy and Rapid Diagnostic Tests (RDTs) are majorly used routinely to diagnose malaria in clinical settings. In recent years, molecular diagnosis has emerged as the most sensitive method for malaria diagnosis. This study determined the usefulness of Polymerase Chain Reaction (PCR) in comparison to microscopy (Giemsa stained thick and thin smears) for the diagnosis of asymptomatic malaria in Ilorin, Nigeria. Methods: Th e study enrolled 310 school children aged 4–15 years with no sign or symptoms of malaria. Blood samples were collected for identification of Plasmodium species infection using light microscopy and conventional PCR. Results: The PCR method detected m o r e infection of P. falciparum 107 (34.5%) than slide microscopy 81 (26.1%) in the study. Only P. falciparum was detected by microscopy while PCR detected mono infection of P. malariae (3.2%) and P. ovale (0.6%) and mixed infection of P. falciparum and P. malariae (3.2%). Overall the PCR method detected more malaria parasite compared to microscopy. Conclusion: The PCR technique, although more laborious and expensive than microscopy, have better diagnostic accuracy and are highly useful for the detection of P. falciparum and other malaria species in asymptomatic and low parasitaemia cases.