In this article we explore the speech layers of a transcription toolkit. We begin by discussing issues of transcription theory and practice, including the difference between broad and narrow phonetic transcription and the importance of narrow transcription with disordered speech, and the measurement of transcriber reliability. We also look at extending symbol sets and using instrumental approaches to deal with atypical speech production. Both segmental and prosodic transcription are dealt with in turn and illustrated with sample transcriptions. We note that, while several phenomena can be subsumed under the prosodic layer, less agreement exists on how to transcribe these than with segmental examples, and that little agreement yet exists on how to notate prosodic disorders. We conclude with illustrations from various adult and child cases.