Background: Only a small number of studies on computerized cytomorphometry have been performed for thyroid FNAC. The present study aimed to determine the usefulness of computerized cytomorphometry methods to further classify thyroid lesions as benign or malignant and to compare the practicability and value of using Papanicolaou (Pap) and Giemsa stains in thyroid FNAC by evaluating their association to various cytologic nuclear parameters. Methods: Fifty-eight thyroid lesions diagnosed by FNAC and categorized according to the Bethesda system for reporting thyroid cytopathology were evaluated in terms of various cytologic nuclear parameters, including nuclear area (NA), nuclear perimeter (NP), nuclear density (ND), long nuclear diameter (LND), and short nuclear diameter (SND). The Pap- and Giemsa-stained slides were examined separately. Results: In the malignant cases, NA, NP, LND, and SND were higher than in the benign cases for both the Pap and Giemsa stains. NA, NP, LND, and SND were higher in Giemsa than Pap for both the benign and malignant groups. Statistically significant differences were detected between the benign and malignant cases in the AUS category. Conclusions: Computerized cytomorphometry is useful in distinguishing between benign and malignant lesions in thyroid FNAC. The measurement of cytologic nuclear parameters in cases suggestive of AUS may be useful for the probable classification of cases as benign or malignant. Although further studies are needed, in nuclear morphometric assessment of thyroid FNAC, Giemsa staining may be more useful and valuable than the Pap stain because of its association with various cytologic nuclear parameters. Diagn. Cytopathol. 2016;44:902–911. © 2016 Wiley Periodicals, Inc.