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Introduction: The objective of this study was to determine the source of health care funding for heads of households related to the management of severe malaria in children admitted to a Kinshasa reference hospital. Methods: This cross-sectional study was conducted on 1,350 hospitalised children under the age of 15 years treated for severe malaria in Kinshasa reference hospitals from January to November 2011 and the heads of households of these children. Results: Only 46% of heads of households reported having sufficient funds directly available in the household budget. The remaining 54% had to call upon external sources of funding (sale of assets, loans, pawning goods). The use of a loan tended to increase significantly mainly for households with a low (adjusted odds ratio = 6.2), and intermediate socioeconomic status (adjusted odds ratio = 3.8) and for households working in the informal sector (adjusted odds ratio = 2.5). Similarly, the sale of assets was more frequently reported for households working in the informal sector (adjusted odds ratio = 2.4)) and for female heads of households (adjusted odds ratio = 3.9). Conclusion: The management of severe malaria is a burden on household income. The majority of heads of households concerned needs to use external funding sources. A State subsidy for this management would help to reduce the risk of debt and sale of assets, especially for the poorest households.