Introduction: Effective organization and operation of the emergency departments (EDs) is a modern challenge for the Greek health system as heterogeneity can be observed in their operation. Although in some hospitals EDs are housed in modern facilities with high hygiene and safety standards as well as with organized screening systems, unfortunately, this is not a common pattern that can be observed in most cases. Aim: The aim of the present study was to explore and compare the EDs of Thessaloniki, regarding their infrastructure, procedures and health and safety status. Methodology: The study sample consists of eight hospitals of Thessaloniki. The study is based on mixed methodology. Initially, a qualitative approach was undertaken through personal observation of the site and the operation of the EDs via a strictly structured observation form. The recordings were then quantified and were used for grading the hospitals which were subsequently grouped according to similar characteristics. Results: The average score is 0.74 with a range from 0.50 to 0.92. The best-performance was recorded in the health and safety category (0.81), while the lower recordings were related to facilities (0.69) and results for organizational issues (triage) were satisfactory (0.72). Hospitals were categorized into four different groups based on their functional characteristics, indicating apparent heterogeneity in the management and organization. Conclusions: Results suggest the need to identify the degree of divergence of EDs in aspects of organization and explore further ways of achieving convergence. It is therefore necessary to extend this study to the rest of Greece in order to establish the differences further in order to be able to propose the implementation of nation-wide triage method and single mode of management in EDs.