Cardiac involvement is a common and serious problem in multisystem inflammatory syndrome in children (MIS-C). Echocardiographic evaluation of systolic and diastolic function by traditional, tissue Doppler and three-dimensional (3D) echocardiography was performed in consecutive 50 MIS-C patients during hospitalization and age-matched 40 healthy controls. On the day of worst left ventricular (LV) systolic function (echo-1), all left and right ventricular systolic function parameters were significantly lower ( p < 0.001), E/A ratio was significantly lower, and averaged E/e′ ratio was significantly higher (median 1.5 vs. 1.8, p < 0.05; 8.9 vs. 6.3, p < 0.001 respectively) in patients compared to control. Patients were divided into 2 groups according to 3D LV ejection fraction (LVEF) on the echo-1: Group 1; LVEF < 55%, 26 patients, and group 2; LVEF ≥ 55%, 24 patients. E/e′ ratio was significantly higher in group 1 than group 2 and control at discharge (median 7.4 vs. 6.9, p = 0.005; 7.4 vs. 6.3, p < 0.001 respectively). Coronary ectasia was detected in 2 patients (z score: 2.53, 2.6 in the right coronary artery), and resolved at discharge. Compared with group 2, group 1 had significantly higher troponin-I (median 658 vs. 65 ng/L; p < 0.001), NT-pro BNP (median 14,233 vs. 1824 ng/L; p = 0.001), procalcitonin (median 10.9 vs. 2.1 µg/L; p = 0.009), ferritin (median 1234 vs. 308 µg/L; p = 0.003). The most common findings were ventricular systolic dysfunction recovering during hospitalization, and persisting LV diastolic dysfunction in the reduced LVEF group at discharge. Coronary artery involvement was rare in the acute phase of the disease. Also, in MIS-C patients, the correlation between LV systolic dysfunction and markers of inflammation and cardiac biomarkers should be considered. Supplementary Information The online version contains supplementary material available at 10.1007/s00246-021-02738-3.