Microscopy has been the most common technique for the diagnosis of malaria in south western Nigeria. This study was undertaken to determine the efficiency of PCR for malaria diagnosis in south western Nigeria. A total of 450 samples submitted for malaria diagnosis at Obafemi Awolowo University Teaching Hospital Complex (OAUTHC), Ile-Ife between the months of January and December, 2009 were used. Methods used included Giemsa staining procedure for estimation of parasite densities and polymerase

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... hain reaction (PCR) to detect the presence of malaria parasite in the whole blood. Using microscopy as reference gold standard, patients comprising 120 males and 330 females with age ranging between less than 1 and 60 samples were used. In all, about 255 (56.7 %) of the samples were positive for microscopy, while 75 (16.7 %) with high parasitaemia on microscopy were positive for PCR analysis. The study concluded that PCR for diagnosis of malaria has sensitivity of 29.4% and specificity of 100% using crude method of DNA extraction while the use of DNA extraction kit has sensitivity of 90.2% and specificity of 100%, hence effort should be geared towards increasing the sensitivity and reduce the cost of doing the test in low resource country like Nigeria. Running Title: Polymerase Chain Reaction in the Diagnosis of Malaria