Alarming discoveries have shown that some pathogenic bacteria have become resistant to all antibiotics (Block 2001). Many threatening microbial assaults have been witnessed, such as ‘mad cow’ disease (bovine spongiform encephalitis [BSE]) caused by prions emerging unexpectedly and spread around the world by international transportation of people and animals (Block 2001). Man and horses are the most ‘frequent flyers’ in international travel (Ostlund 2001). The use of insufficiently disinfected endoscopes during a prepurchase examination might spread infection and have serious consequences (McEvoy et al. 1998). A contaminated cannula resulted in an infection in 3 human patients following arthroscopic meniscus repair (Blevins et al. 1999). In the past, it was difficult to prove a casual relationship between a contaminated instrument and a subsequent nosocomial infection. However, state-of-the-art clinical epidemiology using molecular typing tools (pulsed-field gel electrophoresis, genome sequencing) can prove a causal relationship between the use of reprocessed but still contaminated instruments and cross-infection between patients (Widmer and Frei 1999). A thorough understanding of sterilisation and disinfection measures are necessary to prevent infection. Utilising current healthcare techniques to provide a desirable environment for the equine patient at a reasonable cost for the investor (clinic owner) is not an easy task. Many techniques developed for human medicine have been adopted by veterinary medicine and design innovations are encouraged to contribute to an equivalent level of performance in veterinary medicine. The goal is to provide and maintain a safe environment for patients, personnel and public. The equine surgeon should have a desire for the highest possible standards, even in private practice, to prevent wound infection (McIlwraith and Turner 1987; Turner and McIlwraith 1989). Quality control of autologous tissues (i.e. skin grafts) or engineered tissue products are not considered in this article and readers are referred to Brockbank and Battjes Siler (2001). The rate of surgical wound infection in veterinary medicine is between 5 and 10% (MacDonald et al. 1994; Vasseur et al. 1998). Infections are a dangerous complication after surgical procedures (Southwood and Baxter 1996; Trostle and Hartmann 1999). Various risk factors for infection after colic surgery have been identified (Honnas and Cohen 1997). Preventing infections is the responsibility of all personnel and surgeons should serve as a role model for proper hygiene techniques (von Hagen 1992). Proper gowning and scrubbing techniques are adequately addressed in most surgery textbooks. Infection prophylaxis in surgery begins with uncontaminated instruments. Exogenous (nonpatient-related) sources of microorganisms are operating room personnel, environment and the air. Advancing technique has developed improved air systems for the surgical suite. Whereas personnel can make only slight improvements, major improvements have been made in the sterilisation of instruments. In order to reuse instruments, they must be properly cleaned, sterilised and stored. Even correct handling of surgical instruments cannot always prevent infections, but validating and documenting properly processed instruments can limit future successful litigation.