As of Sunday, at least 38 of those cases were in New York City, with at least three deaths believed to be linked to the illness reported statewide.
Officials say the majority of patients test negative for the novel coronavirus but positive for antibodies, indicating they had previously had COVID-19.
Related: What parents need to know about the mystery syndrome
Symptoms of PMSIS include persistent fever, rash, abdominal pain and vomiting.
Several other pediatric deaths are currently under investigation.
Health officials say they are still learning how the disease manifests.
New York is helping develop national criteria for identifying and responding to the syndrome at the request of the Centers for Disease Control and Prevention, Cuomo said.
New Jersey is reporting eight possible cases, but no deaths, while Yale New Haven Hospital in Connecticut has reported three cases.
Children elsewhere in the U.S. have also been hospitalized with the condition, which was also seen in Europe.
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