AIM: To provide the expression profile of serine protease SNC19/matriptase and its inhibitor hepatocyte growth factor activator inhibitor type 1 (HAI-1) in normal and malignant tissues of gastrointestinal tract at mRNA level for further study on their correlations with tumor progression and metastasis.METHODS: Total RNAs were prepared from 37 samples of colorectal cancer tissues, 40 samples of gastric cancer tissues, and their adjacent normal tissues. The expression of SNC19/matriptase and HAI-1 in these samples was detected by real-time fluorescent quantitative PCR using glyceraldehyde-3-phosphate dehydrogenase as internal standard, and the clinical significance for the correlation with clinicopathological parameters was evaluated.RESULTS: In gastric cancer tissues the expression of HAI-1and SNC19/matriptase was significantly lower than that in the corresponding adjacent normal tissues (Z= -3.280,P= 0.006; Z= -4.651, P= 0.000). HAI-1:SNC19/matriptase ratio showed no difference between normal and malignant tissues (P＞0.05). Analysis of clinicopathological parameters showed decreased expression of HAI-1 and HAI-1 :SNC19/matriptase ratio associated with stage Ⅲ/Ⅳ gastric tumors as compared to stage Ⅰ/Ⅱ ones (Z= -2.140, P = 0.031;Z = -2.155, P = 0.031), and with lymph node-positive gastric cancer tissues as compared to lymph node-negative ones (Z= -2.081, P= 0.036; Z= -2.686, P = 0.006). The expression of SNC19/matriptase had no relationship with stages and lymph node metastasis (P＞0.05). The expression of HAI-1 and HAI-1:SNC19/matriptase ratio increased in well-differentiated gastric cancer tissues, but there was no statistical significance (P＞0.05). The difference of SNC19/matriptase expression was not significant in gastric cancer tissues of different histological differentiation status (P＞0.05). In colorectal cancer tissues, the expression of HAI-1 and SNC19/matriptase was also markedly lower than that in their adjacent normal tissues (Z= -3.100, P = 0.002; Z= -2.731, P = 0.006),whereas HAI-1:SNC19/matriptase ratio showed no difference. Decreased expression of HAI-1 was associated with increased invasive depth and lymph node metastasis,but there was no statistical significance (P＞0.05). The difference of SNC19/matriptase expression and HAI-1:SNC19/matriptase ratio was not significant in different stages and different lymph node metastasis status (P＞0.05).The expression of SNC19/matriptase, HAI-1 or HAI-1:SNC19/matriptase ratio showed no difference in colorectal cancer tissues of different histological differentiation status(P＞0.05).CONCLUSION: The expressions of SNC19/matriptase and its inhibitor HAI-1 are decreased in gastrointestinal cancer tissues compared to their normal counterparts, and the decreased expression of HAI-1 may correlate with invasion and lymph node metastasis. The possible mechanisms involved need to be further investigated.