Original Research Article Introduction: Larynx is one of the most common sites of head and neck carcinoma. HPV positive oropharyngeal squamous cell carcinoma cases are gradually increasing in number. Compared to oral carcinomas, there is a greater diversity of HPV types are associated with laryngeal carcinomas. Very few studies have addressed the issue of causation regarding HPV and laryngeal carcinoma. The role of HPV in the nasopharyngeal tumours is controversial. HPV positive status is associated with a significant beneficial impact on prognosis. Materials and method: Total 53 patients from ENT department, having laryngeal or nasopharyngeal masses are included in this prospective study. During operation, part of the tissue is taken in phosphate buffer solution for detection of HPV by PCR and part of tissue is taken in formalin for histopathology. Result: Out of 35 cases of laryngeal masses, 32 patients (91.4%) are male, 14 patients (40%) are in 6 th decade, 22 patients (62.86%) are smoker, 20 patients (57.14%) presented with hoarsness of voice, 8 patients (22.86%) have mass in both vocal cord, 21 patients (60%) have moderately differentiated squamous cell carcinoma, 6 (17.14%) have vocal cord nodule, 2 (5.71%) have fibro-epithelial polyp with dysplasia, 2 (5.71%) have dysplasia, 2 (5,71%) have squamous cell papilloma with koilocytic changes. Remaining 2 patients have cavernous haemangioma and inverted papilloma. Out of 18 cases of nasopharyngeal masses, 14 patients (77.78%) are male, 5 patients (27.78%) are in 2 nd decade and 4 patients (22.22%) are in 6 th decade, 9 patients (50%) are smoker, 10 patients (55.56%) presented with swelling in cervical region, fever and weight loss, 9 patients (50%) have undifferentiated non-keratinizing nasopharyngeal carcinoma, 6 patients (33.33%) have nasopharyngeal angiofibroma. Remaining 3 patients have keratinizing squamous cell carcinoma and non-Hodgkin lymphoma. But neither HPV-16 nor HPV-18 is found in any laryngeal or nasopharyngeal cases in this study. Conclusion: Most of the laryngeal masses are diagnosed as moderately differentiated squamous cell carcinoma and most of the nasopharyngeal masses are non-keratinizing nasopharyngeal carcinoma followed by nasopharyngeal angiofibroma. HPV-16, 18 infection may not be a leading cause of laryngeal or nasopharyngeal mass.