The zoo says postmortem testing found Flaco was infected with a virus due to eating feral pigeons which had become part of his diet.
It also found he was exposed to four different kinds of rat poison.
Flaco died last month after he either fell or crashed into a building.
Experts say Flaco's underlying conditions may have caused him to crash, and would have ultimately caused his death had he not crashed.
The Eurasian eagle owl rose to fame after he escaped from the Central Park Zoo in February of last year after vandals damaged his enclosure.
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