The previously reported genetic polymorphisms of the stearoyl-CoA desaturase (SCD1) and sterol regulatory element binding protein-1 (SREBP-1) genes were investigated in Fleckvieh bulls using the PCR-RFLP and AS-PCR methods, respectively. The genomic DNA was obtained from a total of 370 bulls. The frequencies of alleles A and V of the single nucleotide polymorphism in exon 5 of the SCD1 gene (SNP 878C>T) were 0.555 and 0.445, respectively. The AA genotype of SCD1 polymorphism showed a lower content of C18:0 (P < 0.01) and higher contents of C14:1 cis-9 (P < 0.001) and C18:1 cis-9 (P < 0.05) in MSF compared to the VV genotype. The SREBP-1 polymorphism was associated with a higher content of C14:1 cis-9 (P < 0.01) in the LS compared to LL genotype in SCF. The results of this study demonstrated the existence of the polymorphisms in the SCD1 and SREBP-1 genes in the population of Fleckvieh cattle and their associations with the concentrations of several MSF and SCF fatty acids.