Background: Head and neck squamous cell carcinoma ((HNSCC)) is the malignancy of squamous cells (the epidermal layer of skin) in cavities in Head and neck includes: larynx, pharynx, paranasal sinuses and oral cavity. The main goal of this research was to understand the effect of mutations in two important genes (KRAS and BRAF) in RAS/MAP kinase (EGFR) signaling pathway in tumor cells with Head and neck squamous cell carcinoma in Iran.Methods: The present cross-sectional study performed from October 2015 to September 2016 on 40 patients suffering from Head and neck squamous cell carcinoma, all confirmed by pathology department of Imam Khomeini hospital. Tumor samples were achieved from the surgical cancer department of Imam Khomeini hospital and stored in liquid nitrogen until starting tests. The tests done in genetic laboratory of Tehran University of Medical Sciences. Techniques we used in this research, were DNA extraction based on phenol-chloroform approach, Multiplex PCR (M-PCR) to amplify mentioned exons and KRAS/BRAF strip assays to detect mutations in mutated hotspots in exon 2 of KRAS and codon V600E in BRAF gene.Results: In this study, we observed 7 mutations in codons 12 and 13 exon 2 in KRAS gene (about 17.5%) and 4 mutations in codon V600E in BRAF gene (about 10%) of obtained tumor samples. The hotspot mutation in codon 12 were Asp (10%) and Ser (5%) respectively. In BRAF, the most common mutation, as we expected according to other researches, was observed in codon V600E. We also observed that 29 people of these patients were male (about 72.5%) and 11 patients were female (about 27.5%). Moreover, 28 patients were over 50 years, while 7 patients were below the age of 50.Conclusion: The results of this study showed that mutations in genes KRAS and BRAF especially in studied hotspots, and the effects on their molecules in EGFR signaling pathway are important in involving Head and neck squamous cell carcinoma, as other cancers. These findings may be considered in choosing drugs for targeted chemotherapy.