Background and Objectives: Lesions of the thyroid and breast represent the two commonest sources of frozen section in Kuwait. This study investigates the value of intraoperative cytology (IC), preoperative fine needle aspiration cytology (FNAC) and intraoperative frozen section (FS), in improving the diagnostic accuracy of such lesions. Material: Thirty-one breast masses and 45 thyroid lesions were included. Methods: In each case, diagnosis was established by (1) preoperative FNAC, (2) intraoperative IC and (3) FS. Their accuracy was compared to paraffin section diagnosis. Results: Sensitivity of FNAC, IC and FS for breast malignancy was 82.6, 95.8 and 91.7%, respectively, while for thyroid malignancy sensitivity was 68.4, 85.0 and 65%, respectively. All three had 100% specificity and 0% false-positive rates. A 100% diagnostic accuracy was achieved by combined FNAC and IC in breast, and 93.3% with combined IC and FS in thyroid lesions. Conclusion: Intraoperative IC improves the diagnostic accuracy of FNAC and FS in breast and thyroid lesions.