Nusa Tenggara Timur (NTT) is one of the provinces with the number of malaria and stunting are high, especially in high risk groups, among them are children under five. Associationof demographic characteristicsand malaria infection history with stunting nutrition status of children under five yearsin NTT is required to know in order to determine effective interventions to overcome the problem of children under five years. The study uses Riskesdas secondary data in 2013.The sample in this analysis were all children under five in NTT who were selected as sample Riskesdas 2013 and have a height measurement values. Analysis using different test that is t-independent. The results of t-tests showed the average difference of children under five height status among children under five living in urban areas and in rural areas (p = 0.003), the average difference height status of children under five among children under five who have a history of malaria infection and without history of malaria (p = 0.00), and there is no the average difference of children under five height status between male and woman (p = 0.056).There is a difference between the nutritional status of stunting children living in rural areas and urban. And there is a difference between the nutritional status of toddlers with a history of malaria and who have no history of malaria. Control of stunting and malaria in children under fiveneed to be developed, especially in rural areas with a high prevalence of malaria and stunting. cross-sector cooperationis needed to enforce stunting and malaria prevention program to control mosquitoesin cluding malaria and nutritional enhancement and improvement ofenvironmental sanitationin rural areas.