Thyroid nodular lesions are the common clinical problem in the world. A variety of tests have been employed to separate benign from malignant thyroid nodules. These tests include isotope scanning and fine needle aspiration cytology (FNAC). Our research was based on the fact that the comparison of FNAC and thyroid isotope scan in thyroid nodule was not researched in Mongolia. Therefore, we want to evaluate the specimen adequacy of FNAC, and compare its result to thyroid isotope scanning in patients with thyroid nodule. The research was conducted on archive materials of FNAC and thyroid isotope scanning of patients with thyroid nodule who were treated in surgical department of The First Central Hospital from 2012 to 2015, and the statistic analyze was done by using SPSS 20 under the auspices of School of Pharmacy and Bio-Medicine,Department of pathology, Mongolian National University of Medical Sciences. We have collected the FNAC of 807 patients, including 34 patients (4.2%) were males and 773 patients (95.8%) were females. FNA cytology results were interpreted as benign in 495 cases (61.3%), follicular lesion of undetermined significance in 31 cases (3.8%), follicular neoplasm in 9 cases (1.1%) suspicious in 17 cases (2.1%), malignant in 3 cases (0.4%), and unsatisfactory in 252 cases (31%). We have got the result of thyroid isotope scanning of 43 (5.32%) patients out of 807 cases. On thyroid scan, 18 patients (41.9%) having cold nodule were labeled as suspicious for malignancy, 25 patients (58.1%) had hot nodule. The FNA diagnosis of 25 patients with a hot nodule following: 1 patient (4%) with neoplasm, 17 patients (68%) with benign results, 6 patients (24%) had non-diagnostic. The FNA diagnosis of 18 patients (41.9%) with cold nodule following: 1 patient (5.5%) with follicular lesion of undetermined significance, 10 patient (55.5%) with benign, 5 patient (27.7%) with non-diagnostic, 2 patient (11.1%) had malignant. The FNAC results were interpreted as benign in 495 cases (61.3%), malignant in 3 cases (0.4%), and unsatisfactory in 252 cases (31%). Two patients out of 18 patients with cold nodule diagnosed as malignancy by FNAC. The sensitivity and specificity of thyroid isotope scanning was 96% and 16.6%, respectively.