Most estimates of the burden of malaria are based on its direct impacts; however, its true burden is likely to be greater because of its wider effects on overall health. Here we estimate the indirect impact of malaria on children’s health in a case-control study, using the sickle cell trait (HbAS), a condition associated with a high degree of specific malaria resistance, as a proxy indicator for an effective intervention. We estimate the odds ratios for HbAS among cases (all children admitted to Kilifi County Hospital during 2000–2004) versus community controls. As expected, HbAS protects strongly against malaria admissions (aOR 0.26; 95%CI 0.22–0.31), but it also protects against other syndromes, including neonatal conditions (aOR 0.79; 0.67–0.93), bacteraemia (aOR 0.69; 0.54–0.88) and severe malnutrition (aOR 0.67; 0.55–0.83). The wider health impacts of malaria should be considered when estimating the potential added benefits of effective malaria interventions.