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Background: Multisystem Inflammatory Syndrome in Children (MIS-C) is a rare but severe illness associated with SARS-CoV-2 infection. A dysregulated immune response is recognized as the main pathogenic mechanism. Previous studies demonstrated the presence of SARS-CoV-2 RNA in faeces of almost one-third of patients with COVID-19, while data are currently missing about MIS-C., Objectives: to evaluate faecal sample positivity to SARS-CoV-2 in MIS-C and to compare the positivity rate between MIS-C and COVID-19 hospitalised children.  DESIGN: observational descriptive study with prospective patient enrollment., Setting and Participants: the SARS-CoV-2 positivity was evaluated in stool samples obtained in a prospective series of 63 paediatric patients admitted to Regina Margherita Children's Hospital (Azienda Ospedaliero Universitaria - Città della Salute e della Scienza, Turin, Northern Italy) with diagnosis of MIS-C (N. 31) or COVID-19 (N. 32), during the first year of pandemic emergency. The real-time reverse transcription polymerase chain reaction (real-time RT-PCR), was performed using a validated kit measuring 3 target SARS-CoV-2 genes: E gene, N gene, and ORF1ab gene MAIN OUTCOME MEASURES: SARS-CoV-2 stool positivity and concomitant gastrointestinal symptoms., Results: overall, 16/63 (25%) stool samples revealed the presence of SARS-CoV-2 mRNA. In patients with COVID-19, faecal samples were collected 8 days as median (IQR 7) after the presumed viral exposure and were positive in 12/31 (39%; 95%CI 23.2-56.2); among children with MIS-C, stools were collected 27.5 days as median (IQR 26.25) after presumed contact and the positivity rate was 12.5% (95%CI 4.4-27.0) (4/32). More than 80% of the children with MIS-C presented gastrointestinal symptoms, but the frequency of gastrointestinal symptoms in patients with positive stools for SARS-CoV-2 RNA is not higher than patients tested negative (p=0.092)., Conclusions: MIS-C patients frequently experienced gastrointestinal symptoms, confirming the intestinal involvement in MIS-C already described in the literature. The presence of SARS-CoV-2 mRNA in faecal samples is confirmed in more than 10% of MIS-C patients and stool positivity was also detected many days after presumed first contact with the virus. This data suggests the possibility of tracing SARS-COV-2 also in faeces for a better description of its circulation and spread in the environment.