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Background  The disease burden of  Plasmodium falciparum  malaria illness is generally estimated using one of two distinct approaches: either by transforming  P. falciparum  infection prevalence estimates into incidence estimates using conversion formulae; or through adjustment of counts of recorded  P. falciparum -positive fever cases from clinics. Whilst both ostensibly seek to evaluate  P. falciparum  disease burden, there is an implicit and problematic difference in the metric being estimated. The first enumerates only symptomatic malaria cases, while the second enumerates all febrile episodes coincident with a  P. falciparum  infection, regardless of the fever’s underlying cause.    Methods  Here, a novel approach was used to triangulate community-based data sources capturing  P. falciparum  infection, fever, and care-seeking to estimate the fraction of  P. falciparum -positive fevers amongst children under 5 years of age presenting at health facilities that are attributable to  P. falciparum  infection versus other non-malarial causes. A Bayesian hierarchical model was used to assign probabilities of malaria-attributable fever (MAF) and non-malarial febrile illness (NMFI) to children under five from a dataset of 41 surveys from 21 countries in sub-Saharan Africa conducted between 2006 and 2016. Using subsequent treatment-seeking outcomes, the proportion of MAF and NMFI amongst  P. falciparum -positive febrile children presenting at public clinics was estimated.    Results  Across all surveyed malaria-positive febrile children who sought care at public clinics across 41 country-years in sub-Saharan Africa,  P. falciparum  infection was estimated to be the underlying cause of only 37.7% (31.1–45.4, 95% CrI) of  P. falciparum -positive fevers, with significant geographical and temporal heterogeneity between surveys.    Conclusions  These findings highlight the complex nature of the  P. falciparum  burden amongst children under 5 years of age and indicate that for many children presenting at health clinics, a positive  P. falciparum  diagnosis and a fever does not necessarily mean  P. falciparum  is the underlying cause of the child’s symptoms, and thus other causes of illness should always be investigated, in addition to prescribing an effective anti-malarial medication. In addition to providing new large-scale estimates of malaria-attributable fever prevalence, the results presented here improve comparability between different methods for calculating  P. falciparum  disease burden, with significant implications for national and global estimation of malaria burden.    Electronic supplementary material  The online version of this article (10.1186/s12936-019-2830-y) contains supplementary material, which is available to authorized users.

The contribution of non-malarial febrile illness co-infections to Plasmodium falciparum case counts in health facilities in sub-Saharan Africa