Background: Fine needle aspiration cytology (FNAC) of thyroid is one of the most common sites encountered in routine practice and one of the challenges is accurately diagnosing rare malignancies including medullary carcinoma thyroid. Aims: To study the cytological criteria for accurate diagnosis of medullary carcinoma of thyroid and to determine factors causing false negativity. Methods: A retrospective study was conducted in the department of Pathology, at a tertiary care centre in South India, retrieving data from the Laboratory Information System (LIS), on diagnosis of medullary carcinoma of thyroid (MCT). A total of 22 cases of MCT were diagnosed during a period of 5 years from September 2013 to August 2018, on histopathology. Fine needle aspiration cytology (FNAC) was performed in 8 of these cases. However, a second search on LIS revealed 2 more cases under the FNA section, without subsequent biopsies. Results and conclusions: Of the 10 FNA cases, 6 were diagnosed accurately; 4 cases had discordance with diagnosis of colloid adenomatous goiter in 2, a case each of involutional nodule and Hurthle cell neoplasm. All the slides were reviewed along with gross findings of resection specimens wherever available. One case was recategorised as MCT on review. The cause of false negativity in the other 3 included paucicellularity and presence of an adjacent larger involutional nodule with a smaller hidden focus of MCT. One case of oncocytoid variant of MCT was misinterpreted as Hurthle cell neoplasm on FNA. In conclusion, FNAC is a useful and accurate non-invasive method that can be used for diagnosis of MCT. With classical cytological features of plasmacytoid to spindle cells, dispersed chromatin, binucleation and presentation of amorphous material in the background, diagnosis can be made with accuracy. The pitfalls include sampling error, misinterpretation in cases with microfollicular pattern or oncocytic cells.