Objectives: Using commercial assays for high-risk (HR) HPV E6/E7 mRNA we sought to determine the accuracy of testing fine needle aspirates (FNA) of neck cervical lymph nodes and tumor tissue from patients with metastatic oropharyngeal squamous cell carcinomas (OPSCC). Materials and Methods:Tumor tissue which was stained for p16 antigens and FNA from patients with OPSCC in tonsils (n=40), base of tongue (n=30) and other sites of the oropharynx (n=6) were tested for HR HPV E6/E7 mRNA using Aptima assays (Hologic). These samples were also tested for HR HPV DNA using cobas 4800 (Roche) and/or Cervista (Hologic) assays. FNA sample adequacy was determined by qPCR for β-actin.Results: HR HPV mRNA and DNA were detected in 68.4% and 71.4% of FNA samples, respectively, and 96.4% were HPV genotype 16. 81% of tumor tissue samples were positive for p16 staining. 82.2% of FNA samples from patients with p16 positive tumors were positive for HPV mRNA compared to 82.4% for HPV DNA. Agreement between FNA testing for HPV and p16 stained tumors was 84.2% (k=0.59) for mRNA compared to 81.4% (k=0.49) for DNA. For all specimens, agreement was 94.3% (k=0.86) between Aptima mRNA and cobas DNA and 94.3% (k=0.77) between the cobas and Cervista DNA assays. A subset of 35 paraffinembedded primary tumors were extracted and tested in the HPV assays and an equal number of cases were positive for mRNA, DNA and p16. The FNA adequacy rate was 92%. Conclusion:The excellent performance of the Aptima HPV E6/E7 mRNA assays indicate that commercial tests should be validated and used for these purposes.