Stomach cancer is an abundant disease in Korean people. In order to identify the genes associated with stomach cancer risk, association study carried out using single nucleotide polymorphisms (SNPs) as a genetic marker. SNPs of selected candidate genes were allelotyped and haplotyped with normal and patient individual samples of Korean population, using the MassARRAY system that consists of homogeneous reactions of probe extension, MALDI-TOF mass spectrometry and SNP allelotyping software. After 39 SNPs in 18 genes were chosen, they were assayed with 200 normal and 197 patient individual samples. Chi-square and odds ratio tests for allele and genotype showed that 8 SNPs in 3 genes would be linked with stomach cancer. In GENE 1, 329 (G/A), 330a (A/G), 331a (A/T), 331d (C/T), 2066(G/A) and 1288 (A/T) were significantly different between two groups. In GENE 2, GENE 3, 345(A/G) and 547(G/A) was statistically significant (P-value<0.05). Based on each SNP allele frequency data, haplotyping analysis carried out through an EM computer program. Haplotyping analysis suggested another suspicious gene that would be linked stomach cancer. Haplotype 4 (666 C-667c G) of LAMA showed significance level (P-value<0.05). These data show that some single nucleotide polymorphisms and haplotypes consisted of some SNPs are associated with stomach cancer and association study is practically effective.