Multiple gastric cancers are found in 5-15% of all patients with gastric cancer. However, no molecular markers have yet been shown to be clinically useful for predicting which patient will or will not have multiple gastric cancers. Recently, microsatellite instability (MSI) has been identified as a molecular marker for multiple colorectal cancers. To elucidate whether MSI could be used as a molecular marker for multiple gastric cancers, we examined MSI in 38 patients with a single gastric cancer, in 26 patients with synchronous multiple gastric cancers and in 14 patients with metachronous multiple gastric cancers. In the patients with synchronous multiple gastric cancers, 1 of the larger tumors was examined. In the patients with metachronous multiple gastric cancers, the first gastric cancer was examined. Five microsatellite loci, including D17S855, D18S58, D18S61, BAT25 and BAT40, were examined with microsatellite assay. MSI was divided into low frequency of MSI (MSI-L) and high frequency of MSI (MSI-H) by the number of affected loci. MSI-L was detected in 3 of the 38 (8%) patients with a single gastric cancer, in 7 of the 26 (27%) patients with synchronous multiple gastric cancers and in 6 of the 14 (43%) patients with metachronous multiple gastric cancers. MSI-H was detected only in 1 of the 38 (3%) patients with a single gastric cancer. The frequency of MSI-L was significantly higher in patients with multiple gastric cancers, both synchronous and metachronous, than in those with a single gastric cancer (p < 0.05 and p < 0.01, respectively). Patients with MSI(+) gastric cancer developed a significantly higher frequency of secondary gastric cancer, when compared with patients with MSI(-) gastric cancer (p < 0.05). These data suggest that MSI may play an important role in the development of multiple gastric cancers, and it may be used clinically as a molecular marker for the prediction of multiple gastric cancers.