Due to the difficulty of obtaining blood samples, which is the invasive method that is currently used for the detection of spp., alternative diagnostic sampling methods that are effective and non-invasive are needed, particularly for long-term studies. Saliva and stool samples from malaria-infected individuals contain trace amounts of DNA and therefore could be used as alternatives. Malaria was screened using rapid diagnosis tests and confirmed via microscopy. Nested PCR tests targeting the -specific gene were performed for blood, saliva and stool samples that were positive for malaria. Three hundred sixty-seven (367) children were enrolled and eighty (22.22%) were confirmed to be positive for malaria. Matched blood, saliva and stool samples were available for 35 children. By using blood smears as the gold standard for the diagnosis of malaria, our study indicates that DNA was more detectable in blood (100%) than in saliva (22.86%) and stools (14.29%). Applying qPCR to the gene to detect DNA in saliva and stool samples cannot be considered as an alternative to the current malaria detection processes using blood specimens.