On September 11, 2001, Hirsch dashed to the World Trade Center, but got trapped under debris as the South Tower collapsed. Hirsch had broken his ribs but he darted back to work to lead the task of identifying the victims after being extracted from the rubble.
"We will do whatever it takes, for as long as it takes, to identify every victim of this tragedy," he pledged.
Hirsch died of natural causes the medical examiner's office said. No specific cause of death was released. He was 79.
"He worked tirelessly to bring some comfort to the families of those lost," said then-New York Mayor Michael Bloomberg, when Hirsch retired in 2013.
Along with his efforts after the terror attacks, Hirsch was esteemed in the field of forensic pathology.
New York Mayor Bill de Blasio praised Hirsch for "over two decades of scientific innovations."
"The Office of the Chief Medical Examiner conducts a solemn and essential role after so many of our city's tragedies, and we are indebted to Dr. Hirsch for his decades of service at the helm of this agency," the mayor said in a statement.
Elevating the science
During his 24-year career at the city's medical examiner's office, Hirsch became known as the father of modern forensic pathology. A stickler for science with little tolerance for political jockeying, he served under four different mayors after his appointment by Mayor Edward Koch in 1989.
During his tenure, Hirsch created the largest public DNA lab in the country to provide scientific evidence in the justice system.
"Medical Examiners are not law enforcement officials," Hirsch had said. "Our allegiance is to the criminal justice system and to civil rights."
He broke new ground to modernize the office and train upcoming forensic pathologists in the field. He published numerous research articles and contributed to books in the investigation of death.
Hirsch also was a professor and chairman of Forensic Medicine at New York University Medical School.
His program was so popular that the waiting list had exceeded four years.