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Background  Infectious diseases such as tuberculosis (TB), malaria and soil-transmitted helminthiasis continue to impose a significant global health burden and socio-economic impact. Globally, minority indigenous people are disproportionately affected by poverty and are shown to experience a disparate burden of disease and poorer health outcomes than the comparative majority population. Despite these inequalities, countries rarely systematically compile epidemiological data disaggregated by ethnicity to enable the extent of the differential to be quantified.    Methods  The systematic review will be reported in accordance with The Preferred Reporting Items for Systematic Review and Meta- Analyses (PRISMA) guidelines. Systematic searches will be conducted in EMBASE, Medline, Scopus and Web of Science for studies reporting data which enable the prevalence of TB, malaria, and/or soil-transmitted helminth (STH) infections amongst minority indigenous populations within the Southeast Asia Region (SEAR) and Western Pacific Region (WPR) to be calculated.  Where studies provide data on disease prevalence for both minority indigenous and other populations within the same study, a comparative analysis will be undertaken. In addition to a narrative synthesis, where sufficient data are available, a random-effects meta-analysis will be conducted to obtain a pooled estimate value for each disease/infection by country and mortality stratum.  Heterogeneity between studies will be examined using the Cochran’s Q test and quantitatively measured by the index of heterogeneity squared (I 2 ) statistics. The methodological quality of the included studies will be assessed using a modified Newcastle-Ottawa Scale.    Discussion  This systematic review aims to analyse the available data on the prevalence of TB, malaria and STH infections within minority indigenous populations of the SEAR and WPR.    Registration  Open Science Framework registration: osf.io/m6sqc    Supplementary Information  The online version contains supplementary material available at 10.1186/s13643-021-01753-y.

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The prevalence of tuberculosis, malaria and soil-transmitted helminth infection in minority indigenous people of Southeast Asia and the Western Pacific: protocol for a systematic review and meta-analysis