Background: Hospitals must be prepared to deal efficiently and effectively with different emergencies. To accomplish this, several countries have standardized their hospital emergency codes to improve their response capability. This is particularly important in Puerto Rico given that many health professionals, particularly physicians and nurses, provide services in more than one hospital. This study examined the emergency codes and alerts utilized in Puerto Rican hospitals. Objective: To assess hospitals’ level of emergency preparedness and response capability related to the variability of emergency codes and alerts utilized to respond to a situation in Puerto Rico. Method: A survey was conducted to characterize hospital emergency department level of preparedness and response to a mass fatality incident. A total of 39 out of a sample of 44 hospitals participated in the study. Semi-structured questionnaires were administered by the research team to members of each hospital’s administrative staff to explore the following: general hospital characteristics, emergency plans, emergency department capacity, collaborative agreements, personnel training, emergency communications, laboratory facilities, treatment protocols, security, epidemiologic surveillance, equipment and infrastructure. Results: Some hospitals in Puerto Rico use color coded emergency alerts, while others use key words or codes. Single color emergency codes can have different meanings in different hospitals. Conclusions: The findings clearly show that there is a lack of uniformity and clarity in the emergency codes utilized by hospitals in Puerto Rico. Single color codes have diverse meanings in different hospitals. This could adversely affect hospitals’ efficient and effective emergency response.