In the present study, there were differences in RB1 (14.3% vs. 0%), PDGFRA (5.7% vs. 25.0%), CDKN2A (2.9% vs. 25.0%), HRAS (8.6% vs. 0%), NOTCH1 (2.9% vs. 12.5%), AKT1 (0% vs. 12.5%), FGFR3 (2.9% vs. 0%), and FLT3 (0% vs. 12.5%) expression upon comparing HPV-positive tonsil cancers with HPV-negative tonsil cancers, respectively. Here, FGFR3 is linked to tonsillitis.