Abstract-During his activities, the learner usually uses comments, highlights and circles sections to tag consulted digital documents. Therefore, many systems have been developed to annotate different electronic resources, often adapted to specific users and for particular uses of documents. This great variety of annotation systems reveals a lack of a clear strategy of how to compare the developed annotation systems of the literature according to their functionalities. As a result, few works have tried to present comparative studies of these tools. The aim of this article is to provide a study of some annotation tools used by learners in educational practices. Therefore, we present a comparison of functionalities provided by forty annotation systems developed by industry and academia during the last decade. The study further reveals gaps in systems and opportunities for further research.