KISS1 and matrix metalloproteinase-9 (MMP-9) may play important roles as metastasis suppressor and metastasis promoter genes, respectively, in a variety of malignancies. However, there is little information about their possible roles in non-small cell lung cancer (NSCLC). The goals of this study were to determine the mRNA and protein expressions of KISS1 and MMP-9 in NSCLC and their relations to metastasis and prognosis. The mRNA and protein expressions of KISS1 and of MMP-9 protein were detected by in situ hybridization and immunohistochemistry respectively in 85 cases of NSCLC, and their matched lymph node metastases. Expressions of KISS1 mRNA and protein were significantly higher in low TNM stages of NSCLC (I-II) compared to more advanced stages (III-IV) (p<0.05). Moreover, in advanced TNM stages, cases without metastasis had higher KISS1 gene expression compared to those with lymph node metastasis (p<0.05). In contrast, MMP-9 expression was higher in stage III-IV NSCLC cases compared to stage I-II tumors (p<0.05) and higher in NSCLC cases with metastasis than those without metastasis (p<0.05). There was negative correction between KISS1 and MMP-9 protein expression (p<0.01). The 5-year survival rate in cases with higher KISS1 protein expression was significantly higher than in those with low expression (20.9 vs. 2.4%, p<0.01). However, the 5-year survival rate of patients with high MMP-9 protein expression were lower than those with low expression (19 vs. 4.7%, p<0.05). Our data suggest that KISS1 and MMP-9 may serve as potential prognostic and therapeutic markers in lung cancer.