Background and Objectives: Data with more severe mutations of the SARS-CoV-2 virus, compared with the original wild-type strain of COVID-19 disease, were reported worldwide. The study aims to describe the clinical and laboratory manifestations of a multisystem inflammatory syndrome in children (MIS-C) associated with SARS-CoV-2 in the Republic of Kazakhstan and to compare the severity of the disease depending on the time of the circulating variant of SARS-CoV-2 virus. Material and methods: A retrospective, multicentre, nationwide study of 89 children with MIS-C who received inpatient treatment from August 1, 2020, to December 1, 2021. The patients were allocated into two groups: 1(2020)  - 45 children and 2 (2021) - 44 children. Study periods were characterized by the circulation of different strains of the SARS-CoV-2 virus. Results: In children with MIS-C in 2021, acute renal failure, disseminated intravascular coagulation syndrome, and shock were statistically more frequently found, which led to fairly common admittance to the intensive care unit. When comparing laboratory data, the children with MIS-C in 2021 had higher values ​​of inflammation markers: ferritin, procalcitonin, erythrocyte sedimentation rate, leukocytes, and neutrophils. Furthermore, these children had a lower level of lymphocytes than children with MIS-C in 2020. Conclusions: MIS-C is a severe, life-threatening systemic disease characterized by multiple organ damage and important inflammatory changes in laboratory parameters. A more aggressive clinical course of MIS-C in 2021 may be associated with the emergence of new SARS-CoV-2 strains. Keywords: children, MIS-C, variants of SARS-CoV-2