Inactivation of tumor suppressor gene serine-threonine kinase 11 (STKII) in clear cell renal cell carcinoma (ccRCC) has been demonstrated; however, the mechanism of this inactivation remains to be investigated. To investigate whether epigenetic alteration plays a role in the inactivation of STKII in RCC, the present study aimed to investigate the methylation status of the STKII promoter and its association with tumor stage and survival in ccRCC patients. Paraffin-embedded specimens were obtained from 42 ccRCC patients. The specimens were analyzed for the methylation status of the STKII promoter CpG island using methylation-specific polymerase chain reaction. Survival, tumor-node-metastasis (TNM)/American Joint Committee on Cancer (AJCC) stages, and hematological parameters were compared between patients with unmethylated (U), partially methylated (P) and methylated (M) STKJJ promoter. Among the 42 patients, there were 12 (28.6%), 18 (42.9%) and 12 (28.6%) patients in the M, P and U groups, respectively. The methylation status of the STKII promoter was associated with T, N and AJCC stages in RCC. Survival analysis showed that the M group had a significantly shorter survival time compared with the P and U groups. These findings suggested that methylation of the STKII promoter in RCC is a not rare event, and it may have an important role in the pathogenesis of RCC and be a risk factor for the prognosis of RCC.