Background:The annual mortality rate from head and neck squamous cell carcinoma (HNSCC) is over 11,000 worldwide. Squamous cell carcinoma of the head and neck (SCCHN) frequently metastasizes to the regional lymph nodes which are the first site of arrest of tumor cells that have invaded the peritumoral lymphatics, hence the strongest predictor of disease prognosis and outcome.Aim:The present study aims to compare the efficacy of frozen sections (cryosection), step-serial sectioning conventional H and E staining, immunohistochemistry (IHC) and RT-PCR analysis in detection of lymph node micrometastasis.Materials and Methods:A prospective series of 30 patients who were diagnosed with primary squamous cell carcinoma of the oral cavity and underwent surgical treatment including unilateral or bilateral selective neck dissection were considered for the study.Result:Metastatic carcinomatous cells were observed in H and E staining of frozen section in 18 lymph nodes (54%) and in 19 lymph nodes (57%) in step-serial sectioned H and E-stained sections of the 78 lymph nodes from 30 patients. Carcinomatous cells were immunolabeled with pancytokeratin in 18 lymphnodes (54%). CK19 mRNA was detected in 33 lymph nodes of 16 patients. RT-PCR gave positive signals for 24% and 23% of lymph nodes positive by histopathology and immunohistochemistry.Conclusion:Our study demonstrated that RT-PCR is far more sensitive in detection of micrometastasis than any other technique used in routine procedures and immunohistochemistry. Fifty-three percent patients with micrometastasis detected by RT-PCR had large T3/T4 tumors. Prognosis was poor for patients who were positive for micrometastasis detected only by RT-PCR, among which two patients died within a period of 6 months.