The prognosis of pediatric chordomas is difficult to predict based on histology. The objective of this study was to assess the expression of a proliferation marker and adhesion molecules in pediatric chordomas and relate the expressions to outcome. In 8 pediatric chordomas, we calculated the MIB-1 labeling index (LI) by counting the number of MIB-1-positive tumor cells in 100 tumor cells. The grade of expression of E-cadherin and CD44 was calculated by estimating the percentage of tumor cells expressing these markers. MIB-1 LI correlated with tumor recurrence (P = 0.007) and low survival rate (P = 0.007). The expression of E-cadherin correlated with disease-free survival (P = 0.009), tumor recurrence (P > 0.0007), and low survival rate (P > 0.0007). CD44 expression did not correlate with recurrence (P = 0.056) or survival rate (P = 0.056). Our results suggest that MIB-1 LI and expression of E-cadherin are helpful to predict outcome in pediatric chordomas.