BackgroundEvidence from population-based studies on the economic burden imposed by chronic non-communicable diseases (CNCDs) is still sparse in Sub-Saharan Africa. Our study aimed to fill this existing gap in knowledge by estimating both the household direct, indirect, and total costs incurred due to CNCDs and the economic burden households bear as a result of these costs in Malawi.MethodsThe study used data from the first round of a longitudinal household health survey conducted in 2012 in three rural districts in Malawi. A cost-of-illness method was applied to estimate the economic burden of CNCDs. Indicators of catastrophic spending and impoverishment were used to estimate the economic burden imposed by CNCDs on households.ResultsA total 475 out of 5643 interviewed individuals reported suffering from CNCDs. Mean total costs of all reported CNCDs were 1,040.82 MWK, of which 56.8 % was contributed by direct costs. Individuals affected by chronic cardiovascular conditions and chronic neuropsychiatric conditions bore the highest levels of direct, indirect, and total costs. Using a threshold of 10 % of household non-food expenditure, 21.3 % of all households with at least one household member reporting a CNCD and seeking care for such a condition incurred catastrophic spending due to CNCDs. The poorest households were more likely to incur catastrophic spending due to CNCDs. An additional 1.7 % of households reporting a CNCD fell under the international poverty line once considering direct costs due to CNCDs.ConclusionOur study showed that the economic burden of CNCDs is high, causes catastrophic spending, and aggravates poverty in rural Malawi, a country where in principle basic care for CNCDs should be offered free of charge at point of use through the provision of an Essential Health Package (EHP). Our findings further indicated that particularly high direct, indirect, and total costs were linked to specific diagnoses, although costs were high even for conditions targeted by the EHP. Our findings point at clear gaps in coverage in the current Malawian health system and call for further investments to ensure adequate affordable care for people suffering from CNCDs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12913-016-1716-8) contains supplementary material, which is available to authorized users.