Attacks by computer viruses, worm programs, and other hostile software (‘malware’), have become very serious problems for computer systems connected to large communication networks such as the Internet. One potential defense against such attacks is to employ diversity—that is, making each copy of the attacked software different. However, existing diversity techniques do not offer sufficient levels of protection. The invention provides an effective diversity solution by applying tamper resistant software (TRS) encoding techniques, to the communications that take place between software components, with corresponding changes to the code handling those communications. These communications may include, for example, data passed between software routines via parameters or mutually accessible variables, light-weight messages, signals and semaphores passed between threads, and messages passed between software processes. Effective TRS encoding techniques include data-flow encoding and mass-data encoding techniques.