In order to determine how emotions and cognition are experienced during collaborative group work online students' descriptions of their learning experience were interpreted using a qualitative approach. A common feature of these accounts was reference to difficulties and problems. Four main themes were identified from this data set. Two of the themes, "Constraints on autonomy" and "Reflections about collaboration", encapsulate the experience of engaging in group work. The other two themes "Virtual others" and "Communicating online". The "impact on progress and achievement" provide some insight into what is unique about the socio-emotional experience of collaborating online and how it can influence motivation and learning. The findings were considered from two perspectives of the role of emotion in learning: the socio-cognitive model of self-regulated learning and the community of inquiry framework (COI). An interdisciplinary approach was adopted by taking into account recent research in social cognitive neuroscience. Some practical recommendations about the deployment of technologies for group work online and for empowering students' understanding of the value of collaborative learning are made. The value of verbal immediacy practices as a way of counteracting the disembodied nature of the relational experience of others online is discussed. (Contains 1 figure.)