In order to identify reliable molecular markers for prognostic prediction in gastric carcinoma, we evaluated the expression of six molecular markers, namely bFGF, IGF-2, HGF, MMP-9, integrin beta3 and uPA in gastric cancer. There was a significant correlation between the expression of these markers and the depth of tumor invasion, vessel invasion, lymph node and distant metastasis, TNM stage and microvessel density. The average survival time and 5-year survival rate of patients with positive expression of molecular markers was higher than those with negative expression. Multivariate analysis showed that abnormal expression of bFGF, MMP-9 and uPA, as well as depth of invasion, lymph node and distant metastasis and TNM stage were independently related to poor prognosis of gastric cancer. MMP-9, bFGF and uPA are potential candidates for development as clinically applicable molecular prognostic markers for gastric carcinoma, and may be effective therapeutic targets for the disease in the future.