The present paper is one of the first steps taken towards the design of an advanced digital edition of the Pali Nikaya and the Chinese Agama sutras. After presenting the two text corpora in digital form, and linking them by a comparative catalogue, it is possible to encode comparative research using TEI markup. Through the formalism of the markup language the resulting digital edition would tell the user in a consistent and precise way about certain aspects in the relationship between two sutras. It is the researcher alone who decides what aspects to encode and how precisely to do so. The paper outlines (in 1.& 2.) the notion of markup and the reasons for its use in the present case. Then I offer two examples of how research can be encoded into markup. In 3.1 the occurrence of a word or phrase in the Pali and I or Chinese is treated in a comparative fashion. Fully done, this kind of analysis would enable, e.g. a user of the Pali text to know to what degree literal parallel s to her text exist in Chinese. For an example, we look at a gatha from the Za ahan jing (T2.99.120b) and its parallel in the Satpyutta Nikiiya (PTS IV, 218). In 3.2 the content structure of the Arrow sutra in Chinese and Pali is analysed and compared. The results are encoded by way of one markup line that describes the difference between the sutras according to a previously devised matrix. This perspective allows precise, quantifiable statements of differences between the two corpora as a whole, based on structural differences between sutra versions.