Koch served three terms, but after leaving city hall in 1990 he was plagued by health problems and heart disease.
Just last year, he was hospitalized with anemia and later a respiratory infection.
Less than two weeks ago, Koch was admitted to the hospital to be treated for water in his lungs and legs. He was released Saturday only to be readmitted Monday with shortness of breath.
The former mayor passed away around 2am Friday morning of congestive heart failure.
A funeral is planned for Monday.
Ed Koch was 88 years old.