Annotation is a paratextual element of Malay manuscripts that has been little studied. This preliminary investigation draws on recently digitised material to survey the varieties of annotation in both literary and kitab manuscripts, highlighting the significant differences between the two manuscript corpora. The main categories of annotation in literary manuscripts include ownership marks, doodling and probatio pennae, warnings about the contents of the texts, pictorial annotation, and, rarest of all, readers' responses to the text. However, annotation is found in far greater quantities in kitab manuscripts, suggesting that the surau or similar religious establishment was the more definitively literate milieu-in spite of the central importance of oral instruction and of personal relationships between teacher and student. Annotation in kitab manuscripts consists mainly of scholarly glosses, including cross-references to other works or authorities, and translation into Malay, along with notes taken down by a student while being instructed by a teacher, and occasional more personal comments. The article concludes with a case study of annotation in a kitab compendium from the collection of Surau Syeikh Abdurrahman in Lima Puluh Kota, west Sumatra. Digitised as part of an Endangered Archives Programme project, the manuscript is heavily annotated in a number of hands. The earlier annotation, including scholarly references, translation glosses and 'lecture notes', is typical of kitab manuscripts and of Islamic manuscripts more generally. The most recent annotation, dating to the 1990s, reveals an apparent collapse in that pedagogic tradition, most likely related to the controversies of Minangkabau Sufism that occured over the manuscript's life.