BACKGROUND: The aim of this study was to determine the detection of cytokeratin (CK) mRNA in oral squamous cell carcinoma (OSCC) cells and to evaluate the CK relevance for OSCC diagnosis in a brush biopsy test. METHODS: Fifty-two pairs of OSCC cells and normal oral mucosal cells were obtained by brush biopsy from OSCC patients. mRNA was extracted from cell pellets for real-time quantitative reverse transcriptase polymerase chain reaction (RT-qPCR). The over-expression levels of CK 17, CK 19 and CK 20 mRNA in OSCC cells were examined by SYBR green real-time RT-qPCR. RESULTS: Compared to normal mucosal cells, the over-expression of CK 17 mRNA was detectable in 40 OSCC cells (76.9%), that of CK 19 mRNA in 19 (36.5%), while that of CK 20 mRNA was not detectable. Compared with CK 19, the mean value of CK 17 mRNA expression level was significantly higher in all 52 patients (P < 0.02). Moreover, the value of CK 17 was significantly higher in T1 and T2 OSCC patients (P < 0.03, respectively), in patients without metastases of neck lymph nodes (P < 0.04), in stage I and stage II patients (P < 0.03 and P < 0.05, respectively) and in well differentiated OSCC patients (P < 0.05). CONCLUSION: Brush biopsy properly serves for detection of CK mRNA using real-time RT-qPCR. This preliminary study demonstrates the CK 17 possibility for application; however, pivotal studies are encouraged to confirm CK 17 as a diagnostic marker of OSCC in a brush biopsy test.