Zinc homeostasis in cells depends on zinc transporters, which are divided into 2 families: ZnT (SLC30A) and ZIP (SLC39A). In this study, we examined the effect of 20 single nucleotide polymorphisms (SNPs) in 10 genes encoding zinc transporters on blood zinc concentration in Japanese subjects (n = 102). Blood zinc levels were determined by microwave plasma-atomic emission spectrometry, and SNPs were analyzed by polymerase chain reaction followed by restriction fragment length polymorphism analysis. Among the 20 SNPs examined, 3 SNPs (SLC30A3 rs11126936, SLC39A8 rs233804, and SLC39A14 rs4872479) were significantly associated with blood zinc concentration. Individuals with genotype TT and TG in rs11126936 showed significantly higher blood zinc concentrations than those with GG. As for rs233804, individuals harboring the A allele had significantly higher blood zinc concentrations than those without this allele. Furthermore, the genotype TT and TG in rs4872479 had significantly higher blood zinc concentrations than those with GG. Among these three SNPs, combination of SLC30A3 rs11126936 and SLC39A8 rs233804 may strongly affect blood zinc levels. This study is the first comprehensive investigation of the effect of SNPs in genes encoding zinc transporters on blood zinc concentration. Adverse effects of zinc deficiency are reported and above 3 SNPs may be related to genetic susceptibility to zinc deficiency.