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Background Anaemia causes health and economic harms. The prevalence of anaemia in women aged 15–49 years, by pregnancy status, is indicator 2.2.3 of the UN Sustainable Development Goals, and the aim of halving the anaemia prevalence in women of reproductive age by 2030 is an extension of the 2025 global nutrition targets endorsed by the World Health Assembly (WHA). We aimed to estimate the prevalence of anaemia by severity for children aged 6–59 months, non-pregnant women aged 15–49 years, and pregnant women aged 15–49 years in 197 countries and territories and globally for the period 2000–19. Methods For this pooled analysis of population-representative data, we collated 489 data sources on haemoglobin distribution in children and women from 133 countries, including 4·5 million haemoglobin measurements. Our data sources comprised health examination, nutrition, and household surveys, accessed as anonymised individual records or as summary statistics such as mean haemoglobin and anaemia prevalence. We used a Bayesian hierarchical mixture model to estimate haemoglobin distributions in each population and country-year. This model allowed for coherent estimation of mean haemoglobin and prevalence of anaemia by severity. Findings Globally, in 2019, 40% (95% uncertainty interval [UI] 36–44) of children aged 6–59 months were anaemic, compared to 48% (45–51) in 2000. Globally, the prevalence of anaemia in non-pregnant women aged 15–49 years changed little between 2000 and 2019, from 31% (95% UI 28–34) to 30% (27–33), while in pregnant women aged 15–49 years it decreased from 41% (39–43) to 36% (34–39). In 2019, the prevalence of anaemia in children aged 6–59 months exceeded 70% in 11 countries and exceeded 50% in all women aged 15–49 years in ten countries. Globally in all populations and in most countries and regions, the prevalence of mild anaemia changed little, while moderate and severe anaemia declined in most populations and geographical locations, indicating a shift towards mild anaemia. Interpretation Globally, regionally, and in nearly all countries, progress on anaemia in women aged 15–49 years is insufficient to meet the WHA global nutrition target to halve anaemia prevalence by 2030, and the prevalence of anaemia in children also remains high. A better understanding of the context-specific causes of anaemia and quality implementation of effective multisectoral actions to address these causes are needed. Funding USAID, US Centers for Disease Control and Prevention, and Bill & Melinda Gates Foundation.