Errors in the synthesis, assembly and/or processing of glycans provoke a group of metabolic genetic pathologies known as Congenital Disorders of Glycosylations (CDG) that have been described at the moment around 150 types. Galactosemia and fructosemia can cause false-positive results in diagnosis of CDG due to mutation in GALT and ALDOB genes leading to changes in carbohydrate metabolism. The aim of this study was to establish and implement the methods for molecular diagnosis of galactosemia and fructosemia necessary for differential diagnosis of CDG. As a material for the study have been used samples of urine, DBS and DNA collected from 8 patients. Biochemical diagnosis was based on assessing of blood Galactose level, GALT enzyme activity and NMR spectroscopy of urine (Galactose, Galactitol and Fructose-1- phosphate). For molecular genetic diagnosis have been used PCR-RFLP and Sanger sequencing methods necessary for identification of genetic variants in GALT and ALDOB genes. The design of primers characteristic to all exons of GALT and ALDOB genes was created with Primer3 software and checked by NCBI Primer-BLAST. Implementation of the molecular-genetic methods have been done on DNA samples of 8 patients. 7 children was suspected for galactosemia, having liver affection and sepsis (E. coli) after breastfeeding during the first week of life, null or reduced GALT activity and high urine Galactose [28.7-50.7 mol/molCrea] and Galactitol [~10 mol/molCrea]. The last one had clinical features characteristic for fructosemia, but have normal level of fructose-1- phosphate in urine, caused by his refusal to eat fruits. During molecular genetic analysis in patients with galactosemia has been identified p. Q188R mutation in 50% of alleles, followed by p.E203L (25%) and p.K285N (17%). It is noteworthy that 8% of alleles have not been identified yet. In the patient with fructoseemia has been detected a pathological deletion (c.113-1_115del) of 4 nucleotides located in intron-exon junction between intron 2 and exon 3. This mutation could cause skipping of exon sequence during splicing of ALDOB gene, leading to a null activity of the residual enzyme. The obtained results confirmed the efficiency of implemented of molecular-genetic methods in the diagnosis of galactosemia and fructosemia, that can be used successfully in the differential diagnosis of CDG.