Background Intra-operative consultation by frozen section is a procedure which plays a major role in the surgical management of patients with neoplastic and non neoplastic disease. Therefore it is critical to determine efficiency of frozen section performance periodically. Objective To evaluate the accuracy of frozen section tests at different anatomical sites by comparing the frozen section diagnosis with the histological diagnosis. Method We conducted a retrospective study in Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, and compared the results of 47 cases of frozen section with their final permanent section diagnosis during a period of January 2017 to December 2018. Result A total of 47 cases were studied on frozen section while no case was deferred for permanent paraffin section. The indication of frozen section was for presence/ typing of neoplasm in 38 cases (80.75%), clearance of margin in eight cases (17%) and diagnosis of Hirschsprung's disease in one case (2.1%). The overall accuracy of frozen section was 91.4% (43 cases) with 8.5% (four cases) discordant with the diagnosis, reported as false negative. None of the cases were reported as false positive. Sensitivity, specificity, positive predictive value and negative predictive value of frozen section in comparison with permanent section (as gold standard) were 85.18%, 100%, 100% and 83.33% respectively. Conclusion The accuracy of frozen section diagnosis at our institute was 91.4% which can be interpreted as comparable with most national and international studies. The overall error rate is 8.5% which is higher than previously published studies. Experience and training of the pathologist reduce the error rate.