In this retrospective study, we investigated the HPV DNA occurrence in 21 laryngeal and 26 primary lung squamous cell carcinomas. Nonisotopic in situ hybridization (NISH) technique was performed with commercially available digoxigenin-labelled DNA probes for HPV screening. Subtyping for HPV subtypes 6/11, 16/18 and 31/33 was also performed. We observed HPV DNA signals in 10 (47.6%) cases of laryngeal SCC and in only 3 (11.5%) cases of lung SCC. Typing showed signals of HPV 6/11, 16/18 and 31/33 infection in 80%, 40%, 30% of the laryngeal carcinomas, respectively. In the lung, we demonstrated type 16/18 positivity in two and type 6/11 in one of the HPV-positive cases. We found a statistically significant correlation between HPV infection and tumour recurrence (p < 0.035) in laryngeal carcinomas, but not between HPV presence and tumour stage or grade in neither larynx nor lung.