Serum exosomes containing noncoding RNA (ncRNA) play an important role in both physiological and pathological conditions. However, biological function of exosomal ncRNA remains unclear. The aim of the study was to investigate the prognostic and diagnostic values of exosomal ncRNA by comparing the amounts of exosomal miR-21 and HOTAIR in serum of laryngeal squamous cell carcinoma (LSCC) patients with those of polyps of vocal cords, and by determinating whether combined detection of the two molecules could provide useful information in the diagnosis of LSCC. Exosomes were isolated from the serum samples of 52 LSCC patients and those of 49 patients with polyps of vocal cords. TEM and Western blot were applied for the confirmation of isolated exosomes by observing the ultra structure and testing CD63 marker protein, respectively. RT-PCR was performed to detect the expression of miR-21 and HOTAIR in the exosomes. The receiver-operating characteristic (ROC) curve was generated to examine the prognostic value of the two molecules. The expression of exosomal miR-21 and HOTAIR was significantly higher in patients with LSCC than those with vocal cord polyps. There were significant differences of serum exosomal miR-21 and HOTAIR expressions between the advanced T classifications (T3/T4) or clinical stages (III/IV) and the early stages. The patients with lymph node metastasis had higher serum exosomal miR-21 and HOTAIR expressions than those without. There were no differences between patient sex, tumor locations and differentiations. The area under the ROC curve of combined examination of exosomal HOTAIR and miR-21 for diagnosing LSCC was 87.6 %, which was significantly higher than 80.1 % of miR-21 (p = 0.0359) or 72.7 % of HOTAIR (p = 0.0012), showing 94.2 and 73.5 % of sensitivity and specificity, respectively, in differentiating the malignant from benign laryngeal disease. Serum exosomal miR-21 and HOTAIR were significantly correlated with clinical parameters of LSCC, and combined evaluation of their serum expressions may be a valuable biomarker to screen LSCC and might be a promising predicting tool for LSCC patient.