Background: Correlation of intraoperative frozen section diagnosis with final diagnosis can be an important component of an institution's quality assurance process., Methods: We performed a quality assurance review of 1207 frozen section diagnoses from 812 surgical cases performed in the Hamilton Regional Laboratory Medicine Programme during a 6-month period in 2007. We reviewed the frozen section and permanent slides from all potentially discordant cases using a multiheaded microscope to arrive at a consensus pertaining to the type and reason for error. We reviewed the clinical record to determine whether there had been a potential adverse impact on immediate clinical management., Results: Frozen sections were most commonly requested for head and neck, nervous system and female genital tract specimens. Twenty-eight frozen sections (3%) were deferred. We identified 24 discordant diagnoses involving 3% of cases and 2% of specimens. The organ systems showing the greatest frequency of discordance relative to the total number from that system were the nervous system, head and neck, and the lungs. Of the errors identified, most occurred owing to diagnostic misinterpretation, followed by problems related to tissue sampling. There was a potential adverse impact on immediate clinical management in 14 cases., Conclusion: Our results add to the Canadian data on the correlation between frozen sections and permanent sections; we note comparability to the concordance rates reported in the literature.