Alerting providers to public health situations requires timeliness and context-relevance, both lacking in current systems. Incorporating decision support tools into electronic health records may provide a way to deploy public health alerts to clinicians at the point of care. A timely process for responding to Health Alert Network messages sent by the New York City Department of Health and Mental Hygiene was developed by a network of community health centers. Alerts with order sets and recommended actions were created to notify primary care providers of local disease outbreaks. The process, effect, and lessons learned from alerts for Legionella, toxogenic E coli, and measles outbreaks are described. Electronic alerts have the potential to improve management of diseases during an outbreak, including appropriate laboratory testing, management guidance, and diagnostic assistance as well as to enhance bi-directional data exchange between clinical and public health organizations.