Recent public health emergencies involving anthrax, the severe acute respiratory syndrome (SARS), and shortages of influenza vaccine have dramatized the need for restrictive public health measures such as quarantine, isolation, and rationing. Front-line physicians will face ethical dilemmas during public health emergencies when patients disagree with these measures. Patients might request interventions that are not recommended or for which they are not eligible, or they might object to intrusive or restrictive measures. The physician's primary responsibility in such emergencies is to the public rather than to the individual patient. In public health emergencies, physicians need to address the patient's needs and concerns, recognize their changed roles, and work closely with public health officials. Physicians can still work on behalf of patients by advocating for changes in policies and exceptions when warranted and by mitigating the adverse consequences of public health measures. Before an emergency occurs, physicians should think through how they will respond to foreseeable dilemmas arising when patients disagree with public health recommendations.