There is increasing interest, both internationally and in South Africa, in strengthening the relationship between psychoanalytic practice and research. This paper reports on a psychoanalytically oriented doctoral programme offered at the University of the Witwatersrand in South Africa. The programme is described in relation to the broader context of the historical relationship of psychoanalysis to the university as well as to the specific context of the history of psychoanalysis in South Africa. Key challenges of the programme, specifically concerning research tensions and methodological and theoretical tolerance, are subsequently explored. The way these issues played out in a group context illustrates their potential for conflict as well as innovative debate. The paper reflects on how the microcosm of this programme illuminates and problematises some of the broader debates in the field of psychoanalysis.