Background. Malaria and undernutrition remain two major causes of childhood mortality in sub-Saharan Africa, including Ethiopia. The synergetic relationship between undernutrition and infection is widely documented but the relationship with malaria remains controversial. More studies are needed to address this and provide information to develop effective strategies for malaria control and prevention of undernutrition.Objective. To assess the relationship between malaria and chronic undernutrition in children aged 6 - 59 months at Bahir-Dar special zone, Ethiopia.Methods. A facility-based case-control study was employed to assess the relationship between malaria and chronic undernutrition at Bahir-Dar. A total of 621 children aged between 6 and 59 months, with a 1:3 ratio of confirmed malaria cases to controls, were enrolled. Clinical data and anthropometric measurements were taken, and blood film taken and examined. Anthropometric data were converted into nutritional indices using World Health Organization Anthro software version 3.2.2 and exported to SPSS for cleaning and analysis.Results. Prevalence of stunting and underweight was 50.3% and 34.2% among cases, respectively. Stunting and underweight were significantly associated with confirmed cases of malaria after sociodemographic and other variables were controlled. Other important predictors were rural residence, sleeping under long-lasting impregnated nets, and using indoor residual spray.Conclusion. Chronic undernutrition was closely associated with malaria infection. Major predictors for contracting malaria were stunting, underweight, rural residence, not using long-lasting impregnated nets and indoor residual spray, male sex and low educational status of mother/caregiver. Integrated actions targeting these factors are necessary to reduce the prevailing problem.