Protein-energy malnutrition is a serious clinical condition with high prevalence in areas where Plasmodium falciparum is highly endemic such as western Kenya. There is a major need to determine the relationship between PEM and malaria antibody profiles especially in an area where malaria is endemic. The objective of this work, therefore, was to determine the association between PEM and specific malaria antibodies and the potential diagnostic value of the antibodies in children aged between 5 and 59 months. Cross- sectional surveys as well as analysis of sera for specific malaria antibodies were carried out at Asembo Division, Bondo District, Kisumu County, Nyanza Province. A total of sixty villages identified through random sampling with each household as the sampling unit were used for data collection. Two thousand, one hundred and twelve (2112) Children < 5 years of age were sampled in three successive cross- sectional surveys: The first survey included children < 3 years of age while the subsequent two surveys included children < 5 years of age. Anthropometric measurements were carried out followed by finger prick blood sample for assay of antibodies in sera of the study children. Statistical variables (Odds Ratio, at 95% CI) were determined using SPSS 11 and SAS computer packages. Both Multivariate and Bivariate analyses were carried out. Epi-info 2002 package was used to determine anthropometric variables. Demographic variables and malaria parasite counts were determined for all the children sampled. Circumsporozoite Surface Protein (CSP) IgG antibody was found to be significantly associated with stunting and underweight (p<0.05) but not with wasting. Liver Stage Antigen (LSA) IgG antibody was significantly associated with wasting only (p<0.05) while Merozoite Surface Protein (MSP) IgG antibody was not significantly associated with any malnutrition state. The mean concentration of CSP IgG was elevated in stunted, wasted and underweight in comparison to controls. Liverstage antigen 1 IgG was elevated in stunted children only as compared to controls, whereas MSP IgG was low in all PEM cases as compared to controls. Specific Plasmodium falciparum antibody profiles could accurately be used to determine the association between malaria and Protein-Energy Malnutrition.