The ability to diagnose thyroid cancers pre-op or intra-operatively by fine needle aspiration cytology (FNAC) or frozen section (FS) leads to the delivery of appropriate one-stage surgical management. We aim to study the concordance and discordance of FNAC and FS with final histology in thyroid pathologies. All thyroid procedures from 2007 to 2011(n = 423), involving FNAC and or frozen section in their management pathway were included. FNAC (n = 159) were classified in a five-tier system (Nondiagnostic, Benign, Atypical, Suspicious or Malignant). FS (n = 128) were classified as inconclusive, benign, suspicious or malignant. FNAC and FS were correlated with final histopathology. 159 out of 423 patients had FNAC (PPV 85.1 %), 26 inadequate specimens noted, benign cytology 57, atypical (n = 23), follicular neoplasm (n = 27), suspicious for malignancy (n = 16) and malignant 11. 13 out of 27 follicular neoplasm and 6 of atypical FNAC cases showed malignancy in their final histopathology. Frozen sections; total of 126 patients had intra-operative frozen section biopsies performed. Overall 105 out of 126 FS biopsies were benign; 21 malignancies detected intraoperatively. Three FS were inconclusive and reported benign in final histopathology. Overall, FNAC demonstrated a PPV of 66.6 % and NPV of 84.6 %. FS demonstrated PPV and NPV of 76.1 and 85.7%, respectively. In conclusion, FNAC is considered as the best modality to triage the thyroid nodule pre-operatively. Atypical and follicular neoplasm cytology categories warrant further clinical assessment and close follow-ups when appear benign. The intra-operative frozen sections are helpful to perform a one-stage operation for suspicious thyroid lesion. This study also highlights the recognised limitation of intra-operative frozen section analysis of thyroid neoplasia.