Automated processes designed to sterilize reusable medical instruments use heat and low-temperature chemicals. Several factors, including the physical properties of the sterilizing agents and whether all of the instruments' surfaces can be adequately cleaned, can cause significant variations in the reliability and effectiveness of the sterilization processes. Instruments exposed to heat-based sterilization processes pose the lowest probability of transmitting diseases between patients. Heat can conduct through many different types of materials and can destroy microorganisms embedded under layers of patient debris. Studies have demonstrated, however, that--unlike heat--low-temperature chemicals require direct contact with the microorganisms to be effective. Moreover, the complex designs of some instruments can adversely affect the low-temperature sterilization processes' outcomes by hindering cleaning and preventing the flow of low-temperature chemicals to all of the instruments' contaminated surfaces. This article will explore the differences between heat-based and low-temperature chemical processes to help health care providers minimize the risk of cross-infection.