This paper explores four issues that have emerged from the research on social, cognitive and teaching presence in an online community of inquiry. The early research in the area of online communities of inquiry has raised several issues with regard to the creation and maintenance of social, cognitive and teaching presence that require further research and analysis. The other overarching issue is the methodological validity associated with the community of inquiry framework. The first issue is about shifting social presence from socio-emotional support to a focus on group cohesion (from personal to purposeful relationships). The second issue concerns the progressive development of cognitive presence (inquiry) from exploration to resolution. That is, moving discussion beyond the exploration phase. The third issue has to do with how we conceive of teaching presence (design, facilitation, direct instruction). More specifically, is there an important distinction between facilitation and direct instruction? Finally, the methodological issue concerns qualitative transcript analysis and the validity of the coding protocol. (Contains 2 figures and 1 table.)