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Analysing trends and levels of the burden of disease at the national level can mask inequalities in health-related progress in lower administrative units such as provinces and districts. We used results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 to analyse health patterns in Indonesia at the provincial level between 1990 and 2019. Long-term analyses of disease burden provide insights on Indonesia's advance to universal health coverage and its ability to meet the United Nations Sustainable Development Goals by 2030.We analysed GBD 2019 estimated cause-specific mortality, years of life lost (YLLs), years lived with disability (YLDs), disability-adjusted life-years (DALYs), life expectancy at birth, healthy life expectancy, and risk factors for 286 causes of death, 369 causes of non-fatal health loss, and 87 risk factors by year, age, and sex for Indonesia and its 34 provinces from 1990 to 2019. To generate estimates for Indonesia at the national level, we used 138 location-years of data to estimate Indonesia-specific demographic indicators, 317 location-years of data for Indonesia-specific causes of death, 689 location-years of data for Indonesia-specific non-fatal outcomes, 250 location-years of data for Indonesia-specific risk factors, and 1641 location-years of data for Indonesia-specific covariates. For subnational estimates, we used the following source counts: 138 location-years of data to estimate Indonesia-specific demographic indicators; 5848 location-years of data for Indonesia-specific causes of death; 1534 location-years of data for Indonesia-specific non-fatal outcomes; 650 location-years of data for Indonesia-specific risk factors; and 16 016 location-years of data for Indonesia-specific covariates. We generated our GBD 2019 estimates for Indonesia by including 1 915 207 total source metadata rows, and we used 821 total citations.Life expectancy for males across Indonesia increased from 62·5 years (95% uncertainty interval 61·3-63·7) to 69·4 years (67·2-71·6) between 1990 and 2019, a positive change of 6·9 years. For females during the same period, life expectancy increased from 65·7 years (64·5-66·8) to 73·5 years (71·6-75·6), an increase of 7·8 years. There were large disparities in health outcomes among provinces. In 2019, Bali had the highest life expectancy at birth for males (74·4 years, 70·90-77·9) and North Kalimantan had the highest life expectancy at birth for females (77·7 years, 74·7-81·2), whereas Papua had the lowest life expectancy at birth for males (64·5 years, 60·9-68·2) and North Maluku had the lowest life expectancy at birth for females (64·0 years, 60·7-67·3). The difference in life expectancy for males between the highest-ranked and lowest-ranked provinces was 9·9 years and the difference in life expectacy for females between the highest-ranked and lowest-ranked provinces was 13·7 years. Age-standardised death, YLL, and YLD rates also varied widely among the provinces in 2019. High systolic blood pressure, tobacco, dietary risks, high fasting plasma glucose, and high BMI were the five leading risks contributing to health loss measured as DALYs in 2019.Our findings highlight that Indonesia faces a double burden of communicable and non-communicable diseases that varies across provinces. From 1990 to 2019, Indonesia witnessed a decline in the infectious disease burden, although communicable diseases such as tuberculosis, diarrhoeal diseases, and lower respiratory infections have remained a main source of DALYs in Indonesia. During that same period, however, all-ages death and disability rates from non-communicable diseases and exposure to their risk factors accounted for larger shares of health loss. The differences in health outcomes between the highest-performing and lowest-performing provinces have also widened since 1990. Our findings support a comprehensive process to revisit current health policies, examine the root causes of variation in the burden of disease among provinces, and strengthen programmes and policies aimed at reducing disparities across the country.The BillMelinda Gates Foundation and the Government of Indonesia.For the Bahasa Indonesia translation of the abstract see Supplementary Materials section.