Hurricane Sandy hit New York City (NYC) on October 29, 2012. Before and after the storm, 73 temporary evacuation shelters were established. The total census of these shelters peaked at approximately 6,800 individuals. Concern about the spread of communicable diseases in shelters prompted the NYC Department of Health and Mental Hygiene (DOHMH) to rapidly develop a surveillance system to report communicable diseases and emergency department transports from shelters. We describe the implementation of this system. Establishing effective surveillance in temporary shelters was challenging and required in-person visits by DOHMH staff to ensure reporting. After system establishment, surveillance data were used to identify some potential disease clusters. For the future, we recommend pre-event planning for disease surveillance.