Background: Electronic health record (EHR) data has been expanding for many years in the US, but use of this data for chronic disease surveillance, program evaluation, and resource allocation is still novel. Objective: Describe two systems the New York City (NYC) Department of Health and Mental Hygiene has developed for collecting EHR data for public health based on existing health IT infrastructure. Methods: The Hub Population Health System is a data system developed with an EHR vendor, eClinicalWorks. It allows the health department to query patient data from participating practices, with results returned as aggregate patient counts. Query Health is a pilot project in collaboration with Healthix, the largest Regional Health Information Organization (RHIO) in New York State. Healthix extracted data on a random sample of patients in the RHIO and loaded this information into a database that the health department could query in aggregate. Results: The Hub system encompasses 750 practices in NYC seeing over 2M patients annually. The Query Health pilot project included data on nearly 300,000 patients at 91 facilities in NYC and Long Island (the Healthix RHIO incorporates data from over 12M patients). While only achieving an 85% nightly reporting success rate, the Hub data is more standardized and comprehensive including essential domains such as vital signs and medications. In comparison, Query Health facilities report a near 100% success rate but with limited completeness across key clinical record domains. Discussion: These systems have provided valuable data to the health department but also demonstrate some limitations of health IT infrastructure in the US. The Hub is limited to a single EHR vendor because of limited interoperability at the time it was developed. RHIOs increase interoperability but participation in RHIOs is still limited and there is much work remaining to ensure that EHR records are standardized and complete.