Introduction: Studies have shown the differential impact of the second surge of acute Covid-19 infection, across age, clinical outcome and ethnicity. How these factors impact the clinical characteristics and outcome of multisystem inflammatory syndrome in children (MIS-C) is largely unknown. Objectives: This hospital based comparative study was undertaken to analyse the clinical characteristics and outcomes of patients admitted with MIS-C during the two waves of Covid-19 infection in a tertiary care teaching hospital in South India. Method: Patients admitted between September 2020 and October 2021 with MIS-C were included in this study. Patient demographics, laboratory values and treatment details were compared between the two surges of COVID 19 related MIS-C.Results: Sixty-five children were admitted with MIS-C in the first wave and 73 in the second wave. More children were referred with a diagnosis of MIS-C in the second wave (p=0.001). There was no significant difference in the mean age or malefemale ratio between the two waves. A significantly higher proportion of children in the second wave had cervical lymphadenitis (p=0.02). Need for intensive care unit (ICU) admission (p<0.001), shock (p<0.001), respiratory support (p<0.001) and multiorgan involvement (p<0.001) were significantly lower in the second wave.