The prognosis of chordomas is difficult to predict based solely on histological findings. The purpose of this study was to assess the immunohistochemical expression of the proliferation marker Ki-67 antigen and the expression of p53 in skull base chordomas and to relate their expressions to the outcome. We examined the expression of p53 and the MIB-1 labeling index (LI), assessed by Ki-67 expression, in 19 tumors (initial, n = 11; recurrent, n = 8) from 11 patients. The correlation among the MIB-1 LI, p53 expression, and the clinical outcome was analyzed. The mean MIB-1 LI and p53 expression at the initial surgery were 5.6 +/- 4.6% and 9.0 +/- 9.4%, respectively. At the time of recurrence, the mean MIB-1 LI and p53 expression were 10.2 +/- 7.4% and 16.5 +/- 12.0%. The correlation between the MIB-1 LI and p53 expression at the initial and recurrent surgeries was highly significant (r = 0.948; P < 0.0001). The change in p53 expression from the initial to the recurrent chordomas was significantly greater in patients who died of tumor-related causes than in the surviving patients. In the surviving patients, the values for MIB-1 LI and p53 expression in the recurrent tumors were significantly higher in the disease-ongoing group than in the disease-free group. Our results suggest that determination of the immunohistochemical expression of p53 and Ki-67 antigen is helpful to predict tumor recurrence and prognosis in skull base chordomas.