Objective:To assess the value of tumor markers(TMs) protein chip diagnostic system C12 in the diagnosis of gastrointestinal cancer(GIC). Methods:The sera of 329 pathologically-confirmed GIC patients were detected by the C12 protein biochip system. The most relevant TMs and the contribution of various combinations of TMs to the improvement of diagnosis were determined. Results:The diagnostic rates of C12 biochip system in 329 GIC patients were 13.73%,33.33%,38.30%,58.03% for stagesⅠ,Ⅱ,Ⅲ and Ⅳ patients,respectively,and the overall diagnostic rate was 39.21%. There were statistically significant difference(P < 0.01) among all clinical stages(contingency table chi-square test), stage Ⅰversus stage Ⅲ,stage Ⅰversus stage Ⅳ,and stage Ⅱ versus stage Ⅳ. The other comparisons didn’t have statistical significance(P > 0.05). Among all the 12 TMs,the top three positive rates of 27.36%,19.76% and 19.45% were obtained from CEA,CA242 and CA19-9,respectively,which were correlated with the stage of GIC. Conclusion:The C12 biochip diagnostic system has some value in the diagnosis of advanced GIC,but its sensitivity for early stage is poor. The miniature and effective diagnostic system is needed in clinic urgently.