On September 30, 2014, the first US patient with Ebola virus disease was diagnosed. Hospitals and healthcare systems identified many complex issues that needed to be addressed to prepare for possible future outbreaks. Here we summarize themes identified in free text responses from a query of infectious disease physicians from the Infectious Disease Society of America's (IDSA) Emerging Infections Network (EIN) early in the domestic Ebola response and place them into the context of biopreparedness for possible future events. We queried infectious disease physician members of the EIN from October 21-November 11, 2014, about their institutions' experience with Ebola preparedness at that time. Of 1,566 EIN physicians, 869 replied to this query, and 318 provided 448 write-in comments in response to the question, "What gaps have been identified in order for facilities to safely care for suspected Ebola patients?" or in a section for general comments. Six themes emerged from the responses: the unique challenges faced by small community hospitals (87 comments), the burden placed on infectious disease and infection control staff (61), ethical questions and planning for vulnerable populations (40), misinformation and stigma (29), financial issues faced by response staff (27), and long-term sustainability (16). This qualitative analysis provides insights into early thinking about challenges in preparing for Ebola and other emerging infections in the United States. The themes identified here should be considered during local, state, and national planning.