This paper focuses primarily on the methodological considerations of a study investigating the interactions of pairs of disabled and non-disabled children working together on computer-based tasks, in mainstream primary schools in Cyprus. Twenty dyads of pupils (each pair comprising a disabled child and a non-disabled peer), were observed and videotaped while working together at the computer. Extensive piloting of data collection strategies, coding schemes and methods of analysis led to the use of Transana, a computer-based qualitative analysis tool, for much of the analysis. Firstly, the analysis involved extracting two 'video transcripts' which were synchronized with the video; one for non-verbal interaction (events) and one for verbal interaction. Two coding schemes were then developed, one for each transcript. The next stage of the analysis involved identification of specific verbal interaction patterns within the non-verbal (event) phases, in respect to collaboration and inclusion, as documented by specific video clips synchronized with both transcripts. The authors believe that this work is unique in applying Transana in this context and it is suggested that the approach has much to offer researchers seeking to understand the fine grain of interactions in inclusive classrooms.