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BACKGROUND: Nationwide household transitions to the use of clean-burning cooking fuels are a promising pathway to reducing under-5 lower respiratory infection (LRI) mortality, the leading cause of child mortality globally, but such transitions are rare and evidence supporting an association between increased clean fuel use and improved health is limited. OBJECTIVES: This study aimed to investigate the association between increased primary clean cooking fuel use and under-5 LRI mortality in Ecuador between 1990 and 2019. METHODS: We documented cooking fuel use and cause-coded child mortalities at the canton (county) level in Ecuador from 1990 to 2019 (in four periods, 1988–1992, 1999–2003, 2008–2012, and 2015–2019). We characterized the association between clean fuel use and the rate of under-5 LRI mortalities at the canton level using quasi-Poisson generalized linear and generalized additive models, accounting for potential confounding variables that characterize wealth, urbanization, and child health care and vaccination rates, as well as canton and period fixed effects. We estimated averted under-5 LRI mortalities accrued over 30 y by predicting a counterfactual count of canton-period under-5 LRI mortalities were clean fuel use to not have increased and comparing with predicted canton-period under-5 LRI mortalities from our model and observed data. RESULTS: From 1990 to 2019, the proportion of households primarily using a clean cooking fuel increased from 59% to 95%, and under-5 LRI mortality fell from 28 to 7 per 100,000 under-5 population. Canton-level clean fuel use was negatively associated with under-5 LRI mortalities in linear and nonlinear models. The nonlinear association suggested a threshold at approximately 60% clean fuel use, above which there was a negative association. Increases in clean fuel use between 1990 and 2019 were associated with an estimated 7,300 averted under-5 LRI mortalities (95% confidence interval: 2,600, 12,100), accounting for nearly 20% of the declines in under-5 LRI mortality observed in Ecuador over the study period. DISCUSSION: Our findings suggest that the widespread household transition from using biomass to clean-burning fuels for cooking reduced under-5 LRI mortalities in Ecuador over the last 30 y. [ABSTRACT FROM AUTHOR]