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Software engineering may well be the foundation upon which security of computer systems will be built for the near future. Self-protecting systems, those which have the internal mechanisms to prevent technical assaults on the computer system's integrity are needed to prevent the unauthorized modification or disclosure of information stored and processed within the system. While most time-shared or multi-programmed computer systems do incorporate rudimentary protection mechanisms which prevent accidental damage to the operating system and to other concurrently processing programs, no general system has withstood the technical onslaught of penetration teams authorized to test its security features. The generic flaws found and analyzed by these penetration teams can be traced to poor design criteria and/or poor programming techniques. This paper discusses some of the fundamentals of software engineering needed to be used and extended in building secure computer systems.