BackgroundSoil-transmitted helminth (STH) infection is driven by a complex interaction of demographic, socioeconomic and behavioural factors, including those related to water, sanitation and hygiene (WASH). Epidemiological studies that measure both infection and potential risk factors associated with infection help to understand the drivers of transmission in a population and therefore can provide information to optimise STH control programmes.MethodsDuring October and November 2019, we conducted a cross-sectional survey of the prevalence and intensity of STH infection and associated risk factors among 7710 primary-school-age children from 64 primary schools across 13 districts in Dak Lak province, Vietnam. Quantitative PCR (qPCR) was used to detect and quantify STH infections.ResultsThe predominant STH species was the hookwormNecator americanus(overall cluster-adjusted prevalence of 13.7%), and its prevalence was heterogeneously distributed across surveyed schools (0% to 56.3%). All other STH species had a prevalence of less than 1%. Using mixed-effects logistic regression, we found that the adjusted odds ratio (aOR) was significantly higher for both infection and moderate-to-heavy-intensity infection withN. americanusamong children from multiple ethnic minority groups, compared to children from the majority group (Kinh). Adjusted odds of infection withN. americanuswere also higher in children who reported practising open defecation at school (aOR 1.42, 95% CI 1.05, 1.93,P= 0.02) and in those who had an unimproved household water supply (aOR 1.28, 95% CI 1.04, 1.57,P= 0.02). Conversely, children with a flushing household toilet had a reduced risk of infection (aOR 0.58, 95% CI 0.47, 0.70,P< 0.01), as did those whose primary female carer attended secondary (aOR 0.65, 95% CI 0.51, 0.84,P< 0.01) or tertiary education (aOR 0.39, 95% CI 0.24, 0.63,P< 0.01).ConclusionsThis study is the largest reported prevalence survey of STH infections conducted using qPCR as a diagnostic technique. The findings of higher adjusted odds of infection amongst ethnic minority children highlight that STH control programmes may not be reaching certain population groups and that additional culturally appropriate approaches may be required. Additionally, the associations between specific WASH factors and infection indicate potential programmatic targets to complement preventive chemotherapy programmes.Graphical AbstractSupplementary InformationThe online version contains supplementary material available at 10.1186/s13071-023-05809-x.