In this paper, we concentrate on justifying the decisions we made in developing the TEI recommendations for feature structure markup. The first four sections of this paper present the justification for the recommended treatment of feature structures, of features and their values, and of combinations of features or values and of alternations and negations of features and their values. Section 5 departs briefly from the linguistic focus to argue that the markup scheme developed for feature structures is in fact a general-purpose mechanism that can be used for a wide range of applications. Section 6 describes an auxiliary document called a “feature system declaration” that is used to document and validate a system of feature-structure markup. The seventh and final section illustrates the use of the recommended markup scheme with two examples, lexical tagging and interlinear text analysis.