Fine needle aspiration (FNA) biopsy has been documented as a reliable, cost-effective test, diagnosing different thyroid lesions. However, its sensitivity declines much in some settings. This study aimed to investigate the value of computerized morphometry and DNA ploidy in differential diagnosis of different thyroid epithelial follicular lesions diagnosed on FNA smears. In this study, 68 cases of thyroid FNA were cytologically examined, and classified according to their postthyroidectomy histopathologic diagnosis as follow: 10 cases of nodular goiter, 14 cases of adenomas, 10 cases of follicular carcinoma, 20 cases of papillary carcinoma, 10 cases of anaplastic carcinoma, and 4 cases of poorly differentiated carcinoma. Using Leica Qwin 500 image analysis system, nuclear area as a morphologic variable, and the DNA ploidy, DNA index, and proliferation indices were measured for each case. Sensitivity of FNA in the studied cases was optimum (100%) in papillary carcinomas and anaplastic carcinomas. However, the sensitivity declined sharply in discriminating nodular goiter and follicular adenoma from well-differentiated follicular carcinoma, thus, most of these cases were diagnosed as follicular lesions. A significant difference in mean values of nuclear area was found between benign and malignant lesions, with no statistical differences within the benign group. Aneuploidy was significantly associated with malignancy. Therefore, image analysis may become an important ancillary test in the initial evaluation of patients with thyroid epithelial lesions.