Dengue virus (DENV) infection imposes a major global health burden, with around 100 million symptomatic cases and about 40 000 deaths each year. Despite decades of effort, no direct-acting antivirals are licensed and current vaccines show serotype-dependent and baseline serostatus-dependent efficacy, raising concerns about antibody-dependent enhancement. Early phase therapeutic trials therefore rely mainly on quantitative viraemia as a virological endpoint. However, DENV RNA in blood becomes undetectable soon after presentation, and may be an imperfect surrogate for infectious virus owing to defective interfering particles and continued replication in tissues. The secreted non-structural protein 1 (NS1) correlates with viral replication and disease severity in many studies and remains detectable after virological clearance, making it an attractive complementary biomarker. Here, we review mechanistic and clinical evidence linking NS1 to viral burden, vascular leakage and thrombocytopenia, and summarize data from human challenge studies, natural infection cohorts and pharmacometric modelling. We highlight the extended analytical window and growing availability of quantitative NS1 assays and propose practical analysis frameworks for incorporating NS1 into early phase dengue trials alongside viral RNA. We also discuss limitations, including serotype, immune status and assay-dependent effects and outline priorities for standardization of NS1-based endpoints. This article is part of the Theo Murphy meeting issue 'Evaluating anti-infective drugs'.