Controversy has surrounded the use of liquid chemical germicides to reprocess medical instruments that are damaged by heat sterilization. A review of the literature was performed to assess and compare the efficacy of disinfection and sterilization processes. The results of this review demonstrate that high-level disinfection of thoroughly cleaned endoscopes is not associated with a higher infection rate than is “sterilization.” While there may be a theoretical distinction between the highest level of disinfection and sterilization, thorough cleaning eliminates clinical differences between the two. High-level disinfection is quick, effective, inexpensive, and recommended whenever heat sterilization is not feasible. A low-temperature sterilization process should be considered only if it is comparable in cost to disinfection or if it offers demonstrated advantages without damaging the instrument. Neither disinfection nor sterilization is likely to be effective if the instrument is not cleaned thoroughly after use.