To investigate common chromosomal changes and the LOH frequency of microsatellite loci in primary gastric cancer samples in order to locate the deleted regions in which human gastric cancer related genes might exist Methods Comparative genomic hybridization (CGH) was used to define global chromosomal aberrations in 43 primary gastric tumors Based on the results of CGH, analysis of loss of heterozygosity (LOH) was performed in chromosome 19 in which the loss was first discovered in the gastric cancers The PCR-based approach was used to investigate 22 loci, which are spaced at 1 1-10 9 cM intervals throughout chromosome 19 The amplified PCR fragments were subjected to electrophoresis in PAGE gel and analyzed with Genescan TM and Genotyper TM Results CGH analysis revealed gains in chromosome 3p(8/43), 8q(8/43), 20 [20 (9/43), 20p(7/43), 20q(4/43)], 12q(16/43), 13q(12/43) and losses in 19 [19 (15/43)], 7 [17 (8/43), 17p (10/43)], 16 (10/43) and 1p (11/43) Among the 43 evaluated samples, the most frequent LOH was detected at locus D19S571 (27 81%) Conclusions The tumorigenesis of gastric cancer includes several chromosomal changes The aberration of chromosome 19 was the first common change founded in gastric cancer The region near the D19S571 might harbor potential genes related to the tumorigenesis of gastric cancer To investigate common chromosomal changes and the LOH frequency of microsatellite loci in primary gastric cancer samples in order to locate the deleted regions in which human gastric cancer related genes that might exist Methods Comparative genomic hybridization (CGH) was used to define global chromosomal aberrations in 43 primary gastric tumors Based on the results of CGH, analysis of loss of heterozygosity (LOH) was performed in chromosome 19 in which the loss was first discovered in the gastric cancers The PCR-based approach was used to investigate 22 loci, which are spaced at 1 1-10 9 cM markers over chromosome 19 The amplified PCR fragments were subjected to electrophoresis in PAGE gel and analyzed with Genescan ™ and Genotyper ™ Results CGH analysis are performed in chromosome 3p (8/43), 8q (8/43), 20 [20 (9/43), 20p (7/43), 20q (4/43)], 12q (16/43), 13q (12/43) and losses in 19 [19 (15/43)], 7 [17 (8/43), 17p (10/43)], 16 (10/43) and 1p (11/43) Among t The most frequent LOH was detected at locus D19S571 (27 81%) Conclusions The tumorigenesis of gastric cancer several several chromosomal changes The aberration of chromosome 19 was the first common change founded in gastric cancer The region near the D19S571 might harbor potential genes related to the tumorigenesis of gastric cancer