According to published reports, the first man was discovered dead Friday night on a C train in Washington Heights.
Less than 12 hours later, another man was found dead on a 4 train in Brooklyn.
Police believe both men were homeless and have not said how either died.
Subways will shut down overnight starting later this week to be cleared out and disinfected.
Ken Lovett, Senior Adviser to MTA Chairman & CEO released a statement saying:
"These tragedies are heartbreaking and we are fully cooperating with the NYPD on their investigation. We have repeatedly said the subways are no replacement for shelter and if these two individuals were indeed homeless, as suspected, it's clear more needs to be done by the city to ensure all New Yorkers have access to needed shelter and services."
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