Differences in prevalence and mortality from coronary artery disease (CAD) were observed among the different Israeli ethnic groups. The incidence of CAD in Israel is highest among Ashkenazi Jews and is much lower among Yemenite Jews. In this present study, we selected 15 single nucleotide polymorphisms (SNPs) from 14 candidate genes involved in (1) the renin-angiotensin system, (2) lipid metabolism, (3) cytokines and adhesion molecules, and (4) growth factors, and (5) the coagulation-fibrinolysis system. We analyzed the 15 SNPs in 94 Israeli healthy populations (47 Ashkenazi Jews and 47 Yemenite Jews) obtained from the National Laboratory for the Genetics of Israeli Populations. We applied chip-based MALDI-TOF mass spectrometry as a method for screening multiplexed genotyping of SNPs for ethnic difference in these healthy populations. Among the 15 candidate SNPs, significant differences in allelic frequency were observed in the 1166A>C of the AGTR1 gene, R158C of the Apo E gene, W64R of the ADRB3 gene, S101S of the TIMP 2 gene, and A222V of the MTHFR gene with respect to allele frequency. The incidence of A/C allele of the AGTR1 gene were 0.638/0.362 vs 0.765/0.235, C/T allele in the apo E gene was 0.915/0.085 vs 0.989/0.011, T/C allele of the ADRB3 gene was 0.989/0.0011 vs 0.926/0.074, G/A allele of the TIMP2 gene was 0.974/0.054 vs 0.830/0.170, and C/T allele in the MTHFR gene was 0.521/0.479 vs 0.819/0.181 for Ashkenazi Jews and Yemenite Jews, respectively. We demonstrated an ethnic difference of CAD-associated SNPs in two Israeli healthy populations using MALDI-TOF mass spectrometry. Further study is necessary to prove causal relation with CAD-associated SNPs and the prevalence of CAD.