Over the past few years, the authors have developed a computerised system which records interaction between teachers and pupils in the primary classroom (children aged between 5 to 11 years). Our Classroom Interaction System (CIS) uses software known as 'The Observer' (Noldus Information Technology, 1995) in conjunction with a handheld data entry device. The coding scheme is derived from the work of Galton et al. (1999) and Good and Brophy (1991). The CIS we will describe represents a move away from the paper and pencil techniques and labour-intensive video transcription traditionally used in this field. The system is mobile, easy to internalise, adaptable and allows the researcher to capture interaction between teachers and pupils real-time. Along with these benefits however, there are complexities and dilemmas. This paper will discuss a number of methodological issues which represent real obstacles in the quest for a valid and reliable tool for quantifying interaction in the classroom.