We report the case of a 37-year-old man with human papillomavirus-positive squamous cell carcinoma of the larynx coexisting with chronic myelogenous leukemia. The patient had no history of smoking or alcohol consumption. Within a few months, his rapidly growing tumor was classified as T4aN2cM0. It could be assumed that the rapid increase in the tumor mass, which did not respond positively to treatment, might have been associated with the coexistence of the chronic myelogenous leukemia, which had been found incidentally. Genetic testing revealed the presence of insertion mutation 3020insC within the NOD2 gene, which might be an important genetic predisposing factor, not only for a single tumor such as laryngeal cancer, but also for multiple primary neoplasms. The presence of an NOD2 mutation could significantly worsen the course of the cancer. Therefore, given the relatively high frequency of 3020insC mutations in the general population, it might be reasonable to perform genetic testing on a wider scale for patients with head or neck cancer, particularly in cases that follow an atypical course. It is also worth emphasizing the importance of thorough and periodically repeated laryngeal examinations in patients with chronic leukemia.