Background: Because of its effect on speech and swallowing, laryngeal squamous cell carcinoma is a devastating disease which has been shown to have a poor survival rate. Abundant research is being carried out in search of novel biomarkers that can aid the process of diagnosis and treatment of this disease. FXYD3, a modulator of Na/K-ATPase, is presented as a biomarker in some cancers. FXYD3 expression has been shown to be effected reversely by tumor necrosis factor alpha. Tumor necrosis factor alpha is a pro-inflammatory cytokine proposed to play an important role in tumor promotion and progression. In our study we examined FXYD3 and tumor necrosis factor alpha mRNA expressions, their correlation with each other and with clinicopathologic parameters in tumor tissues and lymph nodes.Methods: We assessed 75 tissue samples and 30 lymph node samples of laryngeal squamous cell carcinoma patients and compared them to 9 adjacent normal tissue samples by quantitative real-time polymerase chain reaction.Results: FXYD3 mRNA expression showed no significant difference among different tissues. We observed significantly lower tumor necrosis factor alpha mRNA expression in laryngeal tumor tissues compared to adjacent normal tissues. FXYD3 showed significant correlations with node metastasis (N factor), differentiation grade, and regional metastasis in lymph nodes. FXYD3 and tumor necrosis factor alpha mRNA levels significantly correlated in tumor and normal tissues.Conclusion: FXYD3 might be involved in the dedifferentiation and metastasis process of laryngeal squamous cell carcinoma. This biomarker has contributed to the aggressiveness and progression of the tumor. Verification of the observed results will need evaluation in a larger group of patients.