In this study we used polymorphic DNA markers to examine 38 patients with gastric carcinoma for loss of heterozygosity (LOH) on five chromosomal arms. The aims were to compare LOH genotyping with the clinicopathologic variables and to identify some genetic differences between early (EGC) and advanced gastric carcinoma (AGC). The frequency of LOH was found in 27 of 38 (71.1%) cases with a low-level LOH in 17 (44.7%) and a high-level LOH (LOH-H) in 10 (26.3%). There was statistical significance found in the differentiation of cells (WD/MD vs. PD [well or moderately differentiated vs. poorly differentiated]), metastasis (absent vs. present), and tumor-node-metastasis stage (I/II vs. III/IV) based on LOH genotyping. The frequency of LOH in the markers of chromosome 6 revealed a significant difference between the early and advanced stages (P=0.043). However, there were no differences in each chromosome or in the number of affected chromosomes with an allelic loss between the histologic types EGC and AGC, except for the frequency of the markers on chromosome 22. These findings suggest that LOH genotyping may be another independent prognostic indicator in gastric carcinoma, that LOH-H, particularly the LOH on chromosome 6, could be associated with an unfavorable prognosis, while the LOH on chromosome 22 may be related to the histologic progression of gastric carcinoma.