The analysis revealed a significantly higher expression of 41 lncRNAs in recurrent and/or metastatic HNSCC patients compared to healthy volunteers with a fold change of 3.2–2.7 × 103 for 21A, Air, Alpha 280, ANRIL, BACE1AS, Dios3os, E2F4 antisense, Emx2os, GAS5, H19, HAR1B, HOXA6as, HULC, Jpx, Kcnq1ot1, KRASP1, lincRNA-RoR, LUST, MALAT1, mascRNA, MEG9, MER11C, ncR-uPAR, NEAT1, NRON, p53 mRNA, PSF inhibiting RNA, PTENP1, RNCR3, SCA8, SNHG1, SNHG3, SNHG4, SNHG6, SRA, ST7OT, TncRNA, Tsix, UCA1, YRNA1 and Zfas1. Here, MEG9 is linked to head and neck squamous cell carcinoma.