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Biogas technology is one of the solutions for improving sanitation, environment, economy and energy conservation especially for smallholder farmers who are applying mixed crop and livestock farming. Indonesia Domestic Biogas Programme (BIRU) has been implemented in DIY since 2009. However, the household digesters that operate effectively only accounts for less than 50% of the total existing digesters in 2017. These problems should be identified and analyzed for more effective implementation and efficient operation of small-sized biogas system in the future. This research applied fault tree analysis (FTA) method to identify failures and evaluated their effects on the operation of small-sized biogas based on processes, physical component, and human factor point of view. Fourty-one sets of BIRU biogas were selected and sampled using stratified purposive random sampling method. Nineteen minimal cut set and three subsystems were defined, which included process failures, infrastructure failures, and human errors. The fault probabilities of the three subsystems were found to be 0.79; 0.59; and 0.96, respectively. It implied that human error gave the highest probability of errors, followed by process failure, while the physical structure of the reactor had been sufficiently well controlled. This study suggested that careful selection on prospective users should be conducted prior to installation, to ensure the motivation of the users in maintaining the reactor in good conditions. Besides, trainings and assistance system are also required to improve the skills of the user to maintain the performance of their reactor.