Aberrant methylations in human gastric cancers were searched for by a genome scanning technique, methylation-sensitive representational difference analysis. Nine CpG islands (CGIs) in the 5' regions of nine genes, LOX, HRASLS, bA305P22.2.3, FLNc (gamma-filamin/ABPL), HAND1, a homologue of RIKEN 2210016F16, FLJ32130, PGAR (HFARP/ANGPTL4/ARP4), and thrombomodulin, were found to be methylated in two gastric cancer cell lines, MKN28 and MKN74, but unmethylated in the normal sample. Their expressions were lost in the two cell lines, and the causal roles of the methylations in gene silencing were shown by treatment with 5-aza-2'-deoxycytidine. In 41 primary gastric cancers, methylations of these CGIs in association with reduced expressions were observed at high incidences (29-41%) for five genes, including LOX and HRASLS, which have been reported to have tumor-suppressive activities. The other four genes were methylated at low incidences (0-7%). By analysis of the numbers of aberrant methylations in individual cancers, a subset of cancers with high prevalence of aberrant methylations was identified, and all of the 11 cancers in the subset were diffuse type. To analyze the possible involvement of decreased fidelity of maintenance methylation in this subset of cancers, aberrant hypomethylations of three normally methylated CGIs were examined. Cancers with high prevalence of hypomethylations of normally methylated CGIs, however, constituted a different subset. It is expected that these nine genes may include important genes in gastric cancer development and would be useful to identify a distinct subset of gastric cancers.