Peritoneal metastasis is the most frequent form of recurrence for advanced gastric cancer. We previously performed a global analysis of the gene expression of gastric cancer cell lines established from peritoneal metastasis with cDNA microarray. One of the up-regulated genes is L-3 phosphoserine phosphatase (L3-PP). We have examined its potential as a novel marker for the detection of peritoneal micrometastasis of gastric cancer. L3-PP mRNA in peritoneal wash in 93 gastric cancer patients was quantified for comparison of carcinoembryonic antigen (CEA) mRNA by means of real-time RT-PCR to predict peritoneal recurrence. The quantity of L3-PP and CEA correlated with wall penetration. Eleven out of 18 cases with peritoneal dissemination were L3-PP+ (61% sensitivity). For three out of 18 cases of peritoneal dissemination, only L3-PP could detect micrometastasis of gastric cancer. Consequently, free cancer cells that cannot be detected by CEA mRNA could be detected using L3-PP mRNA. Although CEA alone was not sufficient, L3-PP and CEA in combination can attain a higher accuracy of detection.