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Malaria and Protein-Energy-Malnutrition (PEM) are two major causes of childhood mortality in sub-Saharan Africa. Malaria can predispose a child to PEM and the reverse may also be true. Recent studies have presented inconsistent findings about nutritional status and the occurrence of malaria among the children. The goal of this study was to evaluate the association between PEM and malaria parasitemia if any. A case control study in which 90 children diagnosed for PEM (aged 6-59 months), and another well-nourished 90 children age and sex-matched controls were evaluated for malaria parasitemia. A semi-structured proforma was used to obtain relevant information on the children’s sociodemographic characteristics, nutritional indices amongst others. Venous blood sample was collected and thick and thin blood film were prepared and viewed under the microscope. Malaria parasitemia was present in 82 (91.1%) of malnourished group and 12 (13.3%) of the well-nourished group (P<0.05 OR=66.62). Malaria parasitemia was highest in those with kwashiorkor and marasmic kwashiorkor compared with underweight. These differences were statistically significant (P<0.05). The study demonstrates that malnourished children have higher degree of malaria parasitemia and are at risk of malaria. It also shows that severe forms of malnutrition are associated with heavier malaria parasitemia. It is therefore recommended that all malnourished children should have access to use of Insecticide Treated Nets (ITN), malaria chemoprophylaxis as well as empiric treatment of malaria in endemic areas where access to malaria parasite diagnosis is difficult.