This paper explores the theoretical issues surrounding clinical phonetic transcription which are pertinent to the education of speech and language therapy students. It draws on theoretical literature and practical experience, to consider issues of rationale, timing, structure, and content of courses in phonetic transcription for clinical purposes, and explores the problems and pitfalls inherent in the process. It is not a tutorial in clinical practical phonetics, but an examination of the issues which teachers of the subject need to consider in delivering such courses.