Fine needle aspiration (FNA) plays a significant role in the diagnosis of thyroid lesions due to its simplicity and low cost. Hashimoto's thyroiditis (HT) is the second most common thyroid lesion next to endemic goitre diagnosed on FNA in iodine (I2) deficient areas. Data on its incidence, prevalence and clinicopathological features in I2 deficient areas is scanty compared to I2 sufficient areas. In the present study the patients presented with HT a decade earlier than reported in I2 sufficient areas. Presentation as a nodular thyroid is common. Diagnosis of HT is likely to be missed in smears showing cytological evidence of hyperplasia or abundant colloid. HT was concurrent in 20 cases of endemic goitre. Careful screening for Hurthle cell change and lymphocytic infiltration into follicular cells should be carried out. In equivocal cases multiple punctures and immunological investigations are helpful. In antibody-negative cases repeat FNA at follow-up is useful. Marked lymphocytic infiltration and Hurthle cell change may indicate a hypothyroid state but hormonal levels are required for clinical management.