In CSCL research, collaboration through chat has primarily been studied in dyadic settings. This article discusses three issues that emerged during the development of a multi-dimensional coding procedure for small-group chat communication: (a) the unit of analysis and unit fragmentation, (b) the reconstruction of the response structure and (c) determining reliability without overestimation. Threading, i.e. connections between analysis units, proved essential to handle unit fragmentation, to reconstruct the response structure and for reliability of coding. In addition, a risk for reliability overestimation was identified. Implications for analysis methodology in CSCL are discussed.