Electronic health records (EHRs) are increasingly being adopted to improve quality of care in health care systems, but they also have potential to monitor health at the population level. Enhancing existing surveillance methods with innovative EHR use allows for strategic targeting of health resources, and data to guide and evaluate public health initiatives and policies. New York City is currently developing the NYC Macroscope, aggregating EHR data into a surveillance tool to inform public health decisions. We have outlined key issues in developing an EHR-based surveillance system, and proposed indicators for the NYC Macroscope.