This chapter provides an overview of recent advances in molecular diagnostics of head and neck tumors, emphasizing their impact on diagnostic precision, classification, and treatment. It discusses the molecular landscape of squamous cell carcinomas, highlighting distinctions between HPV/EBV-related and non-viral tumors. Key genetic and epigenetic alterations across sinonasal, nasopharyngeal, salivary gland, mesenchymal, and odontogenic tumors are summarized, illustrating how Next-Generation Sequencing (NGS), RNA sequencing, and DNA methylation profiling enhance tumor characterization. The chapter also addresses practical challenges in molecular diagnostics such as tissue quality, fixation, and decalcification, and explores future directions, including liquid biopsy, AI integration, and personalized medicine. Collectively, molecular pathology is reshaping head and neck tumor diagnostics, improving prognostication and enabling targeted therapies.