Background In Denmark, emergency departments (EDs) are replacing acute surgical and medical units. The aim of this study was to compare the trajectory of patients undergoing surgery on the suspicion of appendicitis in a surgical assessment unit (SAU) and EDs with an observation unit, respectively. The primary outcome measure was the time from hospital arrival-to-decision for surgery. Materials and methods A comparative retrospective study with a cross-sectional design and a before-and-after design was carried out during January 2011 to December 2012 at a SAU and an ED at a university hospital (U-SAU and U-ED) and at an ED at a regional hospital (R-ED). Data included time of arrival, decision for surgery, surgery and discharge, and number of blood tests. Results In total, 250 patients were included. Time to decision for surgery was 4.50, 4.95, and 4.63 h (P=0.58) in the U-SAU, R-ED, and U-ED, respectively. Time from decision for surgery to start of surgery was 4.60, 3.29, and 4.12 h in the U-SAU, R-ED, and U-ED, respectively. The difference was significant between the U-SAU and R-ED (P=0.05) and between R-ED and U-ED (P=0.03). Time from surgery to discharge from the hospital was 17.88, 19.28, and 15.13 h in the U-SAU, R-ED, and U-ED, respectively. The difference was significant between the EDs (P=0.02). Significantly more blood tests were performed in the EDs than in the U-SAU. Conclusion The introduction of EDs with observation units did not influence time to decision for surgery, but more blood tests were performed. Copyright (C) 2017 Wolters Kluwer Health, Inc. All rights reserved.