Head and neck squamous cell carcinoma (HNSCC) is the major health concern in Indian population. Despite of advanced treatment the mortality rate for this disease has not been improved very much. Current research focused on development of protein marker for the diagnosis and prognosis of HNSCC. The case control study was performed with 125 HNSCC patients and 104 control cases. The level of p50 and I kappa B alpha proteins in serum were evaluated at pre and post therapy by label free real time surface plasmon resonance (SPR) and western blot analysis. The serum p50 concentration were significantly (P < 0.0001) higher at the time of diagnosis i.e. pre therapy (Mean +/- SD = 27.06 +/- 4.88 ng/mu l) as compared to controls (Mean +/- SD = 16.96 +/- 4.04 ng/mu l) while it decline at post therapy (Mean +/- SD = 21.01 +/- 4.98 ng/mu l). Similarly, the concentration of licBcz protein in serum were slightly higher at pre therapy (Mean +/- SD = 8.33 +/- 1.85 ng/mu l) as compared to controls (Mean +/- SD = 7.27 +/- 1.84 ng/mu l) and declined at post therapy (Mean +/- SD = 7.09 +/- 1.24 ng/mu l). The level of p50 was also high at the early stage of the disease. The specificity and sensitivity of p50 proteins obtained from ROC analysis revealed the potentiality to be diagnostic protein marker for HNSCC for its accuracy in the study cohort. (C) 2015 Elsevier Inc. All rights reserved.