The head and neck region encompasses a variety of complex, intricate structures that can give rise to a plethora of epithelial tumors. As novel diagnostic entities and ancillary tests emerge in surgical pathology, translating this expanding knowledge to cytology can be challenging. This review will summarize key developments in diagnosing virus-associated squamous cell carcinomas and salivary gland lesions by fine needle aspiration (FNA). Despite collective efforts to define optimal thresholds for p16 positivity in cytologic material, the performance of p16 remains suboptimal for FNA specimens, with a lack of consensus on the best cutoff. Forthcoming guidelines are expected to recommend HPV-specific assays as first-line testing in FNAs of metastatic nonkeratinizing SCC due to their superior performance in limited material. In salivary cytology, the Milan System for Reporting Salivary Gland Cytopathology recently entered its second edition, retaining the original diagnostic categories. The risks of malignancy for each category have been refined based on published data. While the diagnostic categories are now familiar, several categories warrant special attention to their nuances and pitfalls to improve diagnostic accuracy. Finally, general principles gleaned from advances in both virus-associated squamous cell carcinoma and salivary neoplasia are highlighted, equipping the practicing cytopathologist to approach everyday cases strategically and confidently.