This study was performed to investigate the association between polymorphisms in the ABCG2 (ATPbinding cassette sub-family G member 2), LEPR (leptin receptor) and SCD1 (stearoyl-coenzyme A desaturase 1) genes and milk production traits in Holstein dairy cows in Iran. The analysis was conducted on 816 lactations from 408 Iranian Holstein cows. Genotyping was carried out using the PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) technique. The results of the association study revealed that cows with genotype AC of the ABCG2-Y581S single nucleotide polymorphism (SNP) had lower breeding value for milk yield compared with the AA genotype, but showed significantly higher fat and protein percentages. Cows that were homozygous for allele T at the LEPR-T945M locus had higher breeding value for fat yield than those that were homozygous for the C allele. Regarding the SCD1-A293V SNP, cows with genotype AV produced a higher 305-day milk yield in comparison with cows with the VV genotype. Furthermore, cows that were homozygous for allele V showed a significantly higher protein percentage compared with AA and AV genotypes. The results of this study suggest that these SNPs have the potential to be used in programmes based on genomic selection in Iranian dairy herds. ______________________________________________________________________________________