Research in the field of Computer Supported Collaborative Learning (CSCL) is based on a wide variety of methodologies. In this paper, we focus upon content analysis, which is a technique often used to analyze transcripts of asynchronous, computer mediated discussion groups in formal educational settings. Although this research technique is often used, standards are not yet established. The applied instruments reflect a wide variety of approaches and differ in their level of detail and the type of analysis categories used. Further differences are related to a diversity in their theoretical base, the amount of information about validity and reliability, and the choice for the unit of analysis. This article presents an overview of different content analysis instruments, building on a sample of models commonly used in the CSCL-literature. The discussion of 15 instruments results in a number of critical conclusions. There are questions about the coherence between the theoretical base and the operational translation of the theory in the instruments. Instruments are hardly compared or contrasted with one another. As a consequence the empirical base of the validity of the instruments is limited. The analysis is rather critical when it comes to the issue of reliability. The authors put forward the need to improve the theoretical and empirical base of the existing instruments in order to promote the overall quality of CSCL-research.