DEP domain containing mammalian target of rapamycin (mTOR)-interacting protein (DEPTOR), a recently identified mTOR-interacting protein, is a novel candidate oncogene. Previous studies reveal that high DEPTOR expression is required to maintain PI3K and Akt activation and to inhibit apoptosis. However, its significance in differentiated thyroid carcinoma (DTC) is not yet known. The present study verifies the mRNA and protein expression of DEPTOR in five cell lines, DTC tissues and normal adjacent tissues. Tissue microarrays of 114 DTC patients were used to detect DEPTOR protein expression. The assessment of DEPTOR levels demonstrated that DEPTOR in DTC cells and tissues was significantly increased compared with normal cells and adjacent normal tissues. DEPTOR protein expression was significantly associated with lymph node status, extrathyroid extension and distant metastasis. Patients exhibiting high DEPTOR expression were statistically susceptible to earlier recurrence and poorer survival than those with low expression. Univariate and multivariate analyses showed that DEPTOR expression was an independent prognostic factor for DTC recurrence. In conclusion, our data indicate DEPTOR as a novel prognostic marker for DTC.