The CRISPR‐Cas9 system allows targeted modifications and manipulation of any genomic loci in different cell lines. The basic principle of the method is based on the directing of non‐specific nuclease Cas9 to a specific area in the genome using sgRNA molecule, in which 20 nucleotides (nt) at 5' end is crucial in recognizing the complementary sequence. The advantage of the CRISPR‐Cas9 system is in its simple manipulation and simultaneous action of several CRISPR‐Cas9 complexes guided by different sgRNA molecules. System modifications include the fusion of catalytic domain of effector protein to the inactive nuclease Cas9 (dCas9), thus enabling editing of the genome and epigenome without inducing double stranded break in the DNA molecule. The modification of CRISPR‐Cas9 system, resulted by fusing the DNA sequence encoding the catalytic domain of de novo DNA methyltransferase 3A (DNMT3A) with the DNA sequence encoding the inactive nuclease dCas9 via a flexible Gly4Ser linker, enables targeted methylation of DNA in the genome. The aim of this study was to construct epigenetic editing CRISPR‐Cas9 tool for targeted DNA methylation of MGAT3 gene promoter close to transcription start site (TSS) and to determine the effect of the target region methylation on the regulation of MGAT3 gene expression. Constructs for targeted methylation were successfully assembled by cloning sequences of sgRNA molecules into plasmids. For plasmid constructs cloning the bacterial strain E. coli XL10‐Gold was used. The plasmid constructs were successfully transfected into the BG1 cell line. After the isolation of total RNA, reverse transcription and real‐time polymerase chain reaction (qPCR), the results show no statistically significant reduction in MGAT3 gene expression in the cells transfected with plasmid constructs that contained active DNMT3A, nor in the control samples. Pyrosequencing was not done to prove if the targeted DNA methylation was induced due to the inability of multiplying bisulfite converted DNA from BG1 cells, so the results of qPCR analysis cannot be accepted with confidence.