Background Chemokine receptors are now known to play an important role in cancer growth and metastasis. However, there is little information regarding chemokine expression in gastric cancer. In this study, we examined CXCL12 expression in gastric cancer and also evaluated whether the down-regulation of CXCL12 is due to aberrant methylation of the gene. Methods CXCL12 expression was examined using real-time reverse-transcription polymerase chain reaction (RT-PCR), immunofluorescence, flow cytometry, and immunohistochemistry, and the methylation status of the gene was evaluated by methylation-specific PCR (MSP) in normal gastric and gastric cancer cell lines and 35 primary gastric carcinomas and corresponding nonmalignant gastric tissues. Results The down-regulation of CXCL12 was observed in gastric cancer cell lines and primary gastric carcinomas, while decreased expression of CXCL12 protein was significantly associated with lymph node metastasis and histological grade. And this down-regulation was found to be in accordance with aberrant methylation of the gene. Hypermethylation of the gene was observed in 65.7% (23 of 35) of the primary gastric carcinomas, while it was found in only 11.4% (4/35) of the corresponding nonmalignant tissues. Furthermore, CXCL12 expression was restored in gastric cancer cell lines after treatment with the demethylating agent, 5-aza-2′-deoxycytidine (5-Aza-dC), and demethylation of the highly metastatic cells SGC-7901 induced invasion suppression of the cells. For two CXCL12 receptors, CXCR4 and CXCR7, the mRNA levels remained almost unchanged with the 5-Aza-dC treatment. Conclusions Collectively, our results suggest that the aberrant methylation of CXCL12 frequently occurs in the down-regulation of CXCL12 in gastric cancers and that it may play a role in the metastasis of gastric cancer.