Abstract: Objective To explore histone H3 lysine 27 trimethylation level of genome-wide in gastric cancer patients. Methods Eight cases including tumor tissue and gastric mucosa tissue in gastric cancer patients were collected from Oct,2007 to Jan,2008.For the first time chromatin immunoprecipitation linked to microarrays（ChIP-chip）was adopted to profile the variations in H3K27me3 in CpG island regions in tumor tissue and gastric mucosa tissues.ChIP-qPCR was used to validate the microarray results.Expression analysis by qRT-PCR was performed to confirm correlations between H3K27me3 and gene expression. Results Two hundred and thirty four(71 increased and 161 decreased) genes displayed significant H3K27me3 between tumor cell and gastric mucosa tissue.The results of ChIP-qPCR were coincided well with microarray. Conclusion There is significant difference in H3K27me3 profiling between tumor tissue and gastric mucosa tissue,these novel candidate genes may become potential biomarkers or therapeutic targets.The ChIP-chip technology will help further reveal molecular mechanisms of gastric cancer and discover new therapeutic targets.