To facilitate the use of audio files for annotation purposes, an audio file format, which includes audio data for playback purposes, is augmented with a parallel data channel of line identifiers, or with a map associating time codes for the audio data with line numbers on the original document. The line number-time code information in the audio file is used to navigate within the audio file, and also to associate bookmark links and captured audio annotation files with line numbers of the original text document. An annotation device may provide an output document wherein links to audio and/or text annotation files are embedded at corresponding line numbers. Also, a navigation index may be generated, having links to annotation files and associated document line numbers, as well as bookmark links to selected document line numbers.