Intrahepatic cholangiocarcinoma(ICC) is a highly malignant adenocarcinoma arising from bile duct epithelial cells of the intrahepatic biliary system with early hematogenous and lymphatic extrahepatic spread. The current treatment methods for ICC are far from ideal. Identifying novel effective prognostic biomarkers which might be related to the development and progression of ICC may help provide new therapeutic strategies. Both calcium-binding protein S100A4 and Matrix metalloproteinase-9(MMP-9) are correlated with development and progression of many carcinomas. In the present study, we investigated expression of S100A4 as well as MMP-9 in ICC tissues from 65 patients using immunohistochemistry. The correlation of S100A4 and MMP-9 expression with clinicopathological features and prognosis of patients were analyzed. S100A4 and MMP-9 were positively expressed in 32(49.2 %) and 35(53.8%) patients, respectively. The positive correlation between S100A4 and MMP-9 expression was statistically significant (P = 0.018). S100A4 positive expression was significantly correlated with vascular invasion (P = 0.008), lymph node metastasis (P = 0.029) and the TNM stage (P = 0.008). MMP-9 expression was not found to be correlated with any clinicopathological parameter. Patients with S100A4 positive expression had a significantly poorer overall survival rate than those with S100A4 negative expression (P = 0.000). MMP-9 positive expression was also correlated with poor survival (P = 0.044). However, only S100A4 expression (P = 0.004) and the surgical margin (P = 0.024) were significantly independent prognostic predictors by multivariate analysis. In conclusion, expression of S100A4 is correlated with MMP-9 expression and it could be a useful marker for predicting the progression, metastasis and prognosis of ICC.