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Just as good programming skills involve the knowledge of many design patterns, which developers can combine and apply in various contexts, good debugging skills involve knowledge of bug patterns. Bug patterns are recurring correlations between signaled errors and underlying bugs in a program. This concept is not novel to programming. Medical doctors rely on similar types of correlations when diagnosing disease. They learn to do so by working closely with senior doctors during their internships. Their very education focuses on learning to make such diagnoses. In contrast, software engineers education focuses on design processes and algorithmic analysis. These skills are, of course, important, but little attention is paid to teaching the process of debugging.

"Bug Patterns in Java" presents a methodology for diagnosing and debugging computer programs. The act of debugging will be presented as an ideal application of the scientific method. Skill in this area is entirely independent of other programming skills, such as designing for extensibility and reuse. Nevertheless, it is seldom taught explicitly. Eric Allen lays out a theory of debugging, and how it relates to the rest of the development cycle. In particular, he stresses the critical role of unit testing in effective debugging. At the same time, he argues that testing and debugging, while often conflated, are properly considered to be distinct tasks.

Once laying this groundwork, he then discusses various "bug patterns" (recurring relationships between signaled errors and underlying bugs in a program) that occur frequently in computer programs. For each pattern, the book discusses how to identify them, how to treat them, and how to prevent them.