Background Emergency department (ED) crowding is common and associated with increased costs and negative patient outcomes. The aim of this study was to conduct an in-depth analysis to identify the root causes of an ED length of stay (ED-LOS) of more than six hours. Methods An observational retrospective record review study was conducted to analyse the causes for ED-LOS of more than six hours during a one-week period in an academic hospital in the Netherlands. Basic administrative data were collected for all visiting patients. A root cause analysis was conducted using the PRISMA-method for patients with an ED-LOS > 6 hours, excluding children and critical care room presentations. Results 568 patients visited the ED during the selected week (January 2017). Eighty-four patients (15%) had an ED-LOS > 6 hours and a PRISMA-analysis was performed in 74 (88%) of these patients. 269 root causes were identified, 216 (76%) of which were organisational and 53 (22%) patient or disease related. 207 (94%) of the organisational factors were outside the influence of the ED. Descriptive statistics showed a mean number of 2,5 consultations, 59% hospital admissions or transfers and a mean age of 57 years in the ED-LOS > 6 hours group. For the total group, there was a mean number of 1,9 consultations, 29% hospital admissions or transfers and a mean age of 43 years. Conclusions This study showed that the root causes for an increased ED-LOS were mostly organisational and beyond the control of the ED. These results confirm that interventions addressing the complete acute care chain are needed in order to reduce ED-LOS and crowding in ED's.