Despite the number of infections, hospitalizations, and deaths from influenza each year, developing the ability to predict the timing of these outbreaks has remained elusive. We have developed the Above Local Elevated Respiratory illness Threshold (ALERT) algorithm to help public health practitioners develop simple rules to define a period of increased disease incidence in a given location. The ALERT algorithm defines a period of elevated disease incidence in a community or hospital that systematically collects surveillance data on a particular disease. By defining this period of increased risk, the ALERT algorithm enables fast response to emerging outbreaks in healthcare settings.