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Background Prolonged emergency department length of stay (EDLOS) is a worldwide issue associated with increased mortality, decreased patient satisfaction and poor quality of care. The factors influencing EDLOS have not been comprehensively studied in the context of Swedish EDs. This study's objective is to determine the input-, throughput- and output factors associated with EDLOS, at two urban EDs in Sweden. Methods Data was collected from two hospitals. All patient visits during the two-year study period were included. Patients who left without being seen by a physician were excluded. The explanatory factors included patient characteristics, medical data, and hospital bed occupancy data. Multi-variable linear regression analysis was used to test the associations between the factors and EDLOS. Results The top contributors to prolonged EDLOS were diagnostic imaging, which added between 64 and 149 min of EDLOS, diagnostic testing at central laboratory (53-99 min), followed by intra-ED zone transfer (46-94 min). Arriving during crowding or being admitted during high hospital bed occupancy had a significant but relatively small absolute effect on the outcome. Conclusions Throughput factors had far greater impact on EDLOS than both input- and output factors. Adapting strategies to the structural and procedural characteristics of each setting may enhance the effectiveness of improvement efforts. Clinical trial number Not applicable.