Soil-transmitted helminth (STH) infections are widely distributed in tropical and subtropical areas, including Brazil. We performed a nationwide population-based study including all deaths in Brazil from 2000 to 2011, in which STHs (ascariasis, trichuriasis and/or hookworm infection) were mentioned on death certificates, either as underlying or as associated causes of death. Epidemiological characteristics, time trends and spatial analysis of STH-related mortality were analysed. STHs was identified on 853/12 491 280 death certificates: 827 (97·0%) deaths related to ascariasis, 25 (2·9%) to hookworm infections, and 1 (0·1%) to trichuriasis. The average annual age-adjusted mortality rate was 0·34/1 000 000 inhabitants (95% confidence interval: 0·27–0·44). Females, children <10 years of age, indigenous ethnic groups and residents in the Northeast region had highest STH-related mortality rates. Nationwide mortality decreased significantly over time (annual percent change: −5·7%; 95% CI: −6·9 to −4·4), with regional differences. We identified spatial high-risk clusters for STH-related mortality mainly in the North, Northeast and South regions. Diseases of the digestive system and infectious/parasitic diseases were the most commonly associated causes of death mentioned in the STH-related deaths. Despite decreasing mortality in Brazil, a considerable number of deaths is caused by STHs, with ascariasis responsible for the vast majority. There were marked regional differences, affecting mainly children and vulnerable populations.