BACKGROUND: Despite the almost universal adoption of Integrated Management of Childhood Illness (IMCI) guidelines for the diagnosis and treatment of sick children under the age of five in low- and middle-income countries, child mortality remains high in many settings. One possible explanation of the continued high mortality burden is lack of compliance with diagnostic and treatment protocols. We test this hypothesis in a sample of children with severe illness in the Democratic Republic of the Congo (DRC). METHODS: One thousand one hundred eighty under-five clinical visits were observed across a regionally representative sample of 321 facilities in the DRC. Based on a detailed list of disease symptoms observed, patients with severe febrile disease (including malaria), severe pneumonia, and severe dehydration were identified. For all three disease categories, treatments were then compared to recommended case management following IMCI guidelines. RESULTS: Out of 1180 under-five consultations observed, 332 patients (28%) had signs of severe febrile disease, 189 patients (16%) had signs of severe pneumonia, and 19 patients (2%) had signs of severe dehydration. Overall, providers gave the IMCI-recommended treatment in 42% of cases of these three severe diseases. Less than 15% of children with severe disease were recommended to receive in-patient care either in the facility they visited or in a higher-level facility. CONCLUSIONS: These results suggest that adherence to IMCI protocols for severe disease remains remarkably low in the DRC. There is a critical need to identify and implement effective approaches for improving the quality of care for severely ill children in settings with high child mortality.