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When should a health system turn the corner from vertical to horizonal? Malaria is an example of a disease which has been traditionally approached by vertical systems both within national public health systems and within the research and donor communities, sometimes even partitioning the species of malaria for separate enquiry, strategies and resourcing. This would make sense when the dominant species is accounting for a large share of the disease burden globally and at national levels. However, as malaria elimination efforts begin to show impact, the community is beginning to consider this disease as part of a larger ecosystem of febrile illness. A general modelling approach which could support the development of integrated strategies is proposed along with some preliminary underpinning work using malaria and febrile illness as an example.