Background: Any healthcare facility must be prepared to handle a dramatic increase in deaths that can be produced by a catastrophic disaster. A mass fatality incident (MFI) will significantly increase the usual number of deaths that hospitals or forensic science services can manage on a daily basis. A survey was conducted to assess the hospital emergency department level of preparedness to deal with an MFI. Objective: To examine healthcare facilities level of preparedness for an MFI and morgue capacity. Methods: A total of 39 out of a sample of 44 hospitals participated in the study. Seven questionnaires were administered to explore: hospital general characteristics; emergency plans; equipment and infrastructure; collaborative agreements; personnel trainings; emergency communications; laboratory facilities; treatment protocols; security; and, epidemiologic surveillance. Results: Three-fourths (79.5%) of the healthcare facilities reported having a morgue, their average storage capacity was of three bodies. More than two-thirds (66.7%) of the institutions stated that they could not increase their morgue's capacity. Most installations without a morgue do not possess an agreement with any other institution for the management of bodies. Hospitals have a very limited number of body bags utilized for the handling and transport of bodies. Conclusion: Most of healthcare facilities have morgues, but there are limitations with the current capacity and the lack of resources to increase their capacity in case of a disaster. Management of an MFI must be part of every hospital's emergency plan, and must include collaborative agreements with forensic authorities, emergency management and public health agencies, and the community.