Background and objective Epithelial-mesenchymal transition (EMT) is considered to be one of the major molecular mechanisms inducing tumor invasion and metastasis. The loss of epithelial cell polarity is a hallmark of the EMT process. Epithelial markers such as Claudin are lost in EMT. Snail is a major transcription factor governing EMT. Recent studies about the mechanism of tumor invasion and metastasis has proven that Snail could enhance the ability of many tumors’ invasiveness. The aim of this study is to investigate the expression of Snail and Claudin-3 in non-small cell lung cancer (NSCLC) and its metastatic lymph node with tissue microarray technique, and to explore clinical significance of these two molecules expression in NSCLC. Methods Snail and Claudin-3 proteins were detected in cases of 59 adjacent normal lung tissues, 302 cases of primary NSCLC and 57 cases of lymph node metastatic tissues by MaxVision and EnVision method of immunohistochemical staining respectively. Results The expression of Snail in adjacent normal lung tissues, NSCLC primary foci and metastatic lymph node appeared upward tendency (P<0.05), and the expression of Claudin-3 in adjacent normal lung tissues, NSCLC primary foci and metastatic lymph node appeared weakened (P<0.05). Further more, expression 1evel of Snail and Claudin-3 proteins in NSCLC were related to the histological type (P<0.05). The Spearman correlation analysis showed that the expression of Snail and Claudin-3 was negatively correlated (r=-0.178, P=0.002). Kaplan-Meier survival analysis indicated that factors such as the tumor size, histological type, grading, metastasis, TNM staging, and difference expression between two proteins were associated with the postoperative survival rate of NSCLC patients (P<0.05). Multivariate analysis using Cox regression model identified that the tumor size, histological type, grading, metastasis and TNM staging were independent prognostic factors of NSCLC patients (P<0.05). Conclusion Snail and Claudin-3 may play important roles in invasion and metastasis in NSCLC, So might be employed to evaluate the prognosis of NSCLC patients.