Among ninety selected lncRNAs in HNSCC patients, we observed a statistically significant higher expression in HPV(+) samples in comparison to HPV(−) samples for EGOA, EGOB, HAR1B, and HOXA-AS2 (HOXA3as) and no expression of GAS5-family compared to HPV(−) samples. This evidence concerns the gene HOXA-AS2 and head and neck squamous cell carcinoma.