A lethality-based control system was designed to provide accurate control of a high temperature shout time (HTST) pasteurizer and to process milk products with a lethality equivalent of 161 degrees F (71.67 degrees C) or above for 15 s. This control system provides significant flexibility in operating the process and optimizing functional properties of the food components. Multivariable control of an HTST pasteurizer is implemented by using product total lethality to determine the controller set-points. The equation that relates the temperature and flow rate combinations to the product total lethality, 161 degrees F (71.67 degrees C), 15 s, was modified to permit overprocessing levels specified by plant personnel. By using this equation and the set-point value selected for the other variable, set-point values for the temperature or the flow rate controller were computed. The flow and temperature controllers are integrated into a real-time monitoring and control system. The monitoring and control system includes the multivariable controller, the lethality rate calculation module, statistical monitoring of the total lethality, product flow rate, hot wafer outlet temperature, and holding tube exit temperature measurements, and the display screens for visual inspection of the monitoring tools. This study attempted to achieve compliance of the HTST process operation with the recommended Pasteurized Milk Ordinance by providing a margin between the alarm limits of the monitoring chart and the safety limits.