Introduction and aim. Single nucleotide variants (SNV) of the patatin‐like phospholipase domain‐containing protein 3 (PNP-LA3) gene play an important role in hepatic lipid remodeling and lipogenesis de novo, which is associated with the development of metabolically unhealthy obesity (MUO) and metabolic associated fatty liver disease (MAFLD). The aim of the study was to define the contribution of SNV PNPLA3 gene to the development of MUO, complicated by MAFLD in children. Material and methods. 200 obese children aged 6-18 years were examined. The main group (n=118) was represented by children with MUO. The control group (n=82) consolidated of children with metabolically healthy obesity (MHO). Whole genome sequencing (CeGat) was performed in 31 children of the main and 21 children of the control group. Results. Among obese children, 14 variants of SNV PNPLA3 (rs139051, rs34179073, rs2294918, rs139047, rs779127153, rs2076212, rs738409, rs738408, rs4823173, rs2072906, rs2076213, rs141106484, rs138736228) were identified, including SNV PNPLA3 g.44322818, not described in the dbSNP core database. The role of the following SNV PNPLA3 genotypes in the development of MUO complicated by MAFLD was revealed: rs738409 C/G (Relative risk (RR)=1.71); rs738408 C/T (RR=1.71); rs4823173 G/A (RR=1.57); rs2072906 A/G (RR=1.57) with Sensitivity (Se)=0.63 and Specificity (Sp)=0.72. Conclusion. The contribution to the development of MUO complicated by MAFLD in children is made by the linked association of genotypes: rs738409 C/G, rs738408 C/T, rs4823173 G/A and rs2072906 A/G out of 14 PNPLA3 SNVs diagnosed by us.