OBJECTIVE To investigate the clinical utility of frozen section (FS) analysis performed during partial nephrectomy (PN) and its influence on intra-operative management. METHODS We performed a retrospective analysis of consecutive PN cases from 2010 to 2013. We evaluated the concordance between the intra-operative FS diagnosis and the FS control diagnosis, a postoperative quality assurance measure performed on all FS diagnoses after formalin fixation of the tissue. We also evaluated the concordance between the intra-operative FS diagnosis and the final specimen margin. Operating reports were reviewed for change in intra-operative management for cases with a positive or atypia FS diagnosis, or if the mass was sent for FS. RESULTS A total of 576 intra-operative FSs were performed in 351 cases to assess the PN tumour bed margin, 19 (5.4%) of which also had a mass sent for FS to assess the tumour type. The concordance rate between the FS diagnosis and the FS control diagnosis was 98.3%. There were 30 (8.5%) final positive specimen margins, of which four (13.3%) were classified as atypia, 17 (56.7%) as negative and nine (30%) as positive on FS diagnosis. Intra-operative management was influenced in six of nine cases with a positive FS diagnosis and in one of nine cases with an FS diagnosis of atypia. CONCLUSIONS The relatively high false-negative rate, controversy over the prognosis of a positive margin, and inconsistency in influencing intra-operative management are arguments against the routine use of FS in PN cases.