Objective: To determine the frequencies of five of the most common (59T>G, 202T>C, 314C>T, 508G>A and 1067T>G) single nucleotide polymorphisms (SNPs) of the FUT3 gene in Thai blood donors and examine their associations with the presence or absence of Lewis antigens on red blood cells.Material and Methods: A total of 364 donor specimens from Songklanagarind Hospital and Regional Blood Centre XII Songkhla, Thailand, were recruited for the study. Molecular analysis of each SNP was performed by polymerase chain reaction amplification with sequence-specific primers (PCR-SSP). The Lewis phenotype was investigated in 159 individuals using the standard hemagglutination test.Results: The frequencies of the SNPs were 32.0% (59T>G), 46.6% (202T>C), 21.7% (314C>T), 37.9% (508G>A), and 25.0% (1067T>A). The prevalences of the Lewis phenotype were 61.0% for Le(a-b+), 7.6% for Le(a+b-), 11.3% for Le(a+b+), and 20.1% for Le(a-b-). The Lewis-negative phenotype was significantly associated with homozygosity in 59T>G and 1067T>A (χ2 =49.873, and χ2 =44.520, respectively).Conclusion: Our findings suggest that le59,1067 is largely responsible for the Lewis-negative phenotype in our southern Thai population. Genetic variations in FUT3 polymorphisms may be used as molecular markers for ethnicity and to help understand the roles of the Lewis blood group in infections or clinical diseases.