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Objectives: The goal of this study was to assess if body mass index (BMI) affects the pace of cardiac muscle recovery in children after Pediatric Inflammatory Multisystem Syndrome Temporally Associated with SARS-CoV-2/COVID-19 (PIMS-TS). Methods: A prospective single-center study enrolled consecutive children hospitalized with PIMS-TS between October 2020 and February 2022 and followed up after 6 weeks and 6 months. In all children, three-dimensional echocardiography and global longitudinal strain were used to assess ventricular function and the results were analyzed according to patients' BMI status. Results: This study enrolled 170 patients aged 1–17 years, median 8.5 ± 4.43 years. Children with normal BMI (>5th and <85th percentile; n = 115) accounted for 67.65%, overweight and obese children (>85th percentile; n = 40) accounted for 23.53% and underweight children (<5th percentile; n = 15) accounted for 8.82% of the participants. In all patients, the means of left and right ventricular ejection fractions (LVEF and RVEF) in 3D-ECHO and average GLS were within normal limits at discharge and during follow-up. However, in children with normal weight, the function of the left ventricle improved between 6 weeks and 6 months according to both GLS and LVEF (respectively: LV GLS −20.19 ± 3.88% and −23.17 ± 2.58, p < 0.05; LVEF 60.68 ± 2.64% and 63.58 ± 2.49%, p < 0.05), while no significant improvement was observed in underweight, overweight and obese children. In patients with BMI > 85th percentile, the mean of left ventricular GLS after 6 weeks, although in the normal range, was significantly lower than in underweight children (respectively: −20.09 ± 2.5% and −23.55 ± 3.55%, p = 0.002), whereas left ventricle function assessed with 3D-ECHO showed no significant difference in both groups at that time (BMI > 85th percentile LVEF 61.15 ± 3.21%, BMI < 5th percentile LVEF 61.30 ± 2.71%, p = 0.36). During the study period, right ventricular function remained within normal limits and no significant differences according to both GLS and RVEF were reported between weight status groups. However, further significant right ventricular function improvement between 6 weeks and 6 months was observed in children with normal weight according to GLS (respectively: −22.6 ± 4.51% and −24.16 ± 2.97%, p = 0.02), while RVEF in 3D-ECHO remained unchanged (respectively: 64.01 ± 3.61% and 64.53 ± 3.15%, p = 0.63). In groups of underweight, overweight and obese children, no significant changes between 6 weeks and 6 months were observed (BMI < 5th percentile RVEF at 6 weeks 66.20 ± 2.86% and BMI < 5th percentile RVEF at 6 months 65.20 ± 2.28%, p = 0.58; BMI > 85th percentile RVEF at 6 weeks 63.44 ± 3.00% and BMI > 85th percentile RVEF at 6 months 64.11 ± 2.52%, p = 0.58). Conclusions: Left and right ventricular function stayed within normal limits 6 weeks after PIMS-TS regardless of patients' BMI. Left and right ventricular function improved further between 6 weeks and 6 months after acute disease in the group of children with normal BMI. GLS is a sensitive tool for its assessment. Lower ventricular GLS in children with BMI > 85th percentile may indicate poorer left ventricular performance. Children with normal BMI may present with a more advantageous cardiac recovery pace after PIMS-TS. [ABSTRACT FROM AUTHOR]