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Probabilistic hazard assessments are a fundamental tool for assessing the threats posed by hazards to communities and are important for underpinning evidence based decision making on risk mitigation activities. Indonesia has been the focus of intense tsunami risk mitigation efforts following the 2004 Indian Ocean Tsunami, but this has been largely concentrated on the Sunda Arc, with little attention to other tsunami prone areas of the country such as eastern Indonesia. We present the first nationally consistent Probabilistic Tsunami Hazard Assessment (PTHA) for Indonesia. This assessment produces time independent forecasts of tsunami hazard at the coast from tsunami generated by local, regional and distant earthquake sources. The methodology is based on the established monte-carlo approach to probabilistic seismic hazard assessment (PSHA) and has been adapted to tsunami. We account for sources of epistemic and aleatory uncertainty in the analysis through the use of logic trees and through sampling probability density functions. For short return periods (100 years) the highest tsunami hazard is the west coast of Sumatra, south coast of Java and the north coast of Papua. For longer return periods (500–2500 years), the tsunami hazard is highest along the Sunda Arc, reflecting larger maximum magnitudes along the Sunda Arc. The annual probability of experiencing a tsunami with a height at the coast of > 0.5 m is greater than 10% for Sumatra, Java, the Sunda Islands (Bali, Lombok, Flores, Sumba) and north Papua. The annual probability of experiencing a tsunami with a height of >3.0 m, which would cause significant inundation and fatalities, is 1–10% in Sumatra, Java, Bali, Lombok and north Papua, and 0.1–1% for north Sulawesi, Seram and Flores. The results of this national scale hazard assessment provide evidence for disaster managers to prioritise regions for risk mitigation activities and/or more detailed hazard or risk assessment.