Summary Many patients with human papillomavirus (HPV)-related head and neck squamous cell carcinoma present initially with cervical nodal metastasis. Fine needle aspiration (FNA) of the nodal disease might be the only diagnostic material available for p16 immunohistochemistry (IHC) and HPV testing. The current study aims to evaluate p16 IHC in FNA and establish guidelines for its interpretation. The percentage and intensity of p16 IHC staining were examined in sixty matched FNA and surgical cases. Cytomorphologic features were included in the analysis. P16 IHC staining was correlated with the results seen in the surgical specimens and with HPV-in situ hybridization (ISH). Analysis of different thresholds demonstrated that the threshold of 10% p16 tumor cell positivity had the best overall concordance rate with surgical p16 IHC (kappa = 0.650) and with FNA HPV-ISH (kappa = 0.714). Applying the recommended p16 positivity threshold for surgical specimens (70%) on FNA materials resulted in low sensitivity (39%) and low negative predictive value (26%). In comparison with p16 IHC in surgical specimens, 6/46 FNA cases (13%) were falsely negative for p16. All 6 cases were associated with necrotic background, two (33%) lacked large tumor clusters, and one (17%) had low cellularity. The recommended threshold for p16 IHC on surgical specimens should not be used in cytology materials. The cutoff value for p16 immunostain in FNA specimens showing best results in our series is 10%. When p16 IHC is negative in FNA specimens, a repeat stain on a surgical specimen is recommended to avoid a false negative diagnosis.