Frozen section provides a rapid diagnosis intra or perioperatively that guides the surgeon to make a therapeutic decision for the patient’s health benefit. The comparison between the frozen section diagnosis and permanent section diagnosis is an integral part of quality assurance in surgical pathology. This study was performed to assess the diagnostic accuracy of frozen section at different anatomic sites assuming histopathology as a gold standard. This prospective cross sectional study was performed in the Pathology laboratory adjoining the operation theatre and Department of Pathology S.M.S Medical College and Hospital, Jaipur, during a period of 2 years from January 2017 to December 2018. The results of 170 cases of frozen section were compared with their permanent section diagnosis and analysed. A total of 224 frozen section specimens from 170 cases were studied. The diagnoses were deferred in 4 (1.79%) specimens. Out of remaining 220 specimens, the concordant and discordant diagnostic frequencies were 215 (95.98%) and 5 (2.23%) respectively. Discrepancies were mainly related to misinterpretation, sampling and technical errors. The overall diagnostic accuracy was 97.73%. The sensitivity, specificity, positive predictive value and negative predictive value were 92.68%, 98.88%, 95% and 98.33% respectively. The average turn-around time calculated was 20 minutes. Our study concurred that the frozen section is a rapid, reliable and an accurate technique to guide the surgeons in deciding the best therapeutic approach for the patients. The accuracy rate can be further improved by regular monitoring of frozen section performance.