Whether multiple single nucleotide polymorphisms (SNPs) of BCL11A and HBS1L-MYB genes affect hemoglobin (Hb)F production and hematological parameter variation in β-thalassemia/HbE and homozygous HbE in Thai subjects with low and high HbF levels are still unclear. Three SNPs of BCL11A gene (rs1427407, rs10189857 and rs11886868) and 3 SNPs of HBS1L-MYB gene (rs4895441, rs9399137 and rs28384513) were analyzed in 45 β-thalassemia/HbE patients who had HbF levels lower and higher than 15 %, and in 50 homozygous HbE who had HbF levels lower and higher than 5 %. Their hematological parameters were measured using automated blood counter. The HbF level was analyzed using high performance liquid chromatography (HPLC). There were no statistical significant differences of allele and genotype frequencies of 3 SNPs in the BCL11A gene between the groups of β-thalassemia/HbE patients and homozygous HbE subjects with low and high HbF levels. Significant differences in the allele frequencies in HBS1L-MYB SNP rs4895441 (p = 0.041) and rs9399137 (p = 0.048) were observed in homozygous HbE subjects with HbF £ 5 % and > 5 %. Moreover, significant differences in MCV (p = 0.005) and trends towards significant differences in MCH (p = 0.057) and HbF levels (p = 0.051) were found in HBS1L-MYB SNP rs9399137 of homozygous HbE subjects. Therefore, the HBS11L-MYB SNPs especially rs9399137 had an effect on HbF production and the variation of hematological parameters in homozygous HbE subjects, but not in β-thalassemia/HbE patients.