A onetime high-ranking doctor in the Cook County medical examiner’s office who was fired after an internal review found he botched autopsies — including one in which he failed “to recognize a homicide” — now is facing scrutiny at his job with the coroner’s office in Indianapolis.

The chief forensic pathologist with the Marion County, Indiana, coroner’s office has asked Dr. John E. Cavanaugh’s former bosses in Chicago for details about what led them to boot him and to file a complaint about him with Illinois regulators, records show.

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“I am requesting a copy of the letter regarding Dr. Cavanaugh that was prepared for the Illinois Department of Professional Regulation,” Dr. Christopher Poulos wrote Cook County officials on May 30.

That was three days after the Chicago Sun-Times reported Cavanaugh had been fired in November and that his former boss Dr. Ponni Arunkumar, Cook County’s chief medical examiner, had filed the complaint against him.

“Additionally, I am requesting copies of Dr. Cavanaugh’s autopsy reports that have been amended,” Poulos wrote. “This information will help the operations of the Marion County coroner’s office and allow us to better serve the public.”

Arunkumar’s office provided the Indiana coroner with records from 17 autopsies — including one of a man Cavanaugh found had “no clear evidence of trauma” even though the medical examiner’s office says he had numerous wounds from an assault.

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Cavanaugh ruled that death “undetermined.” Another pathologist reexamined the case and ruled it a homicide, finding Cavanaugh had made numerous errors.

Cavanaugh didn’t return a call seeking comment. Previously, he told the Sun-Times that mistakes he made generally were minor, often involving his inability to master Cook County’s computer system.

Poulos and other Marion County officials would not comment about Cavanaugh, who began working as a pathologist for that agency in 2009. Cavanaugh continued to work weekends for the Marion County coroner during the 10 months he also worked for the Cook County medical examiner, where Arunkumar hired him as her top deputy, then demoted him after five months before later firing him.

In June, an Indianapolis television station reported that police have asked the Marion County coroner to review Cavanaugh’s autopsy finding in the case of an Indiana woman whose death he ruled was “undetermined” though she had head-to-toe injuries and brain trauma. WTHR-13 also reported that Marion County is now “reviewing all of Dr. Cavanaugh’s homicide cases from over the past year” — a step taken after the Sun-Times’ May 27 report.

Arunkumar decided to re-examine every one of Cavanaugh’s 218 Cook County cases after a peer-review process found Cavanaugh had made errors in autopsy reports last year. That unprecedented re-examination is ongoing.

Dr. Ponni Arunkumar, Cook County's chief medical examiner.

Dr. Ponni Arunkumar, Cook County’s chief medical examiner. | Ashlee Rezin / Sun-Times

Officials with the Illinois’ Department of Financial and Professional Regulation — which licenses doctors and can discipline them — would not comment.

“So far, multiple possible violations of professional conduct and deviations from the standards of practice within individual cases, as well as a pattern and practice from case-to-case of professional misconduct, gross incompetence, and a failure to provide appropriate and/or required documentation have been identified,” according to the March 12 letter Arunkumar sent the state agency.

The letter says Cavanaugh’s cases involved “failure to document injuries,” “failure to document portions of an examination,” “issuing reports in which the cause of death on the report does not correspond to the state of Illinois death certificate” and “failure to properly document specimens collected at the time of examination.”

The son of a doctor, Cavanaugh, 60, grew up in Libertyville and now lives in Crown Point, Ind., where he worked for the Lake County, Indiana, coroner’s office from February 2003 until the summer of 2015, when he stopped getting work under his month-to-month contract. His relationship with Coroner Merrilee Frey ended a few months after the Post-Tribune of Northwest Indiana reported Cavanaugh had performed autopsies and testified in criminal trials while his Indiana physician’s license was suspended for a year over his failure to pay state taxes.

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Frey wouldn’t discuss why Cavanaugh stopped working for her or whether she would review the autopsies he did for the Lake County coroner’s office, only that, “The Lake County coroner’s office has a quality assurance process which allows for case review on all cases including homicides, suicides and accidents.”

It’s unclear whether Cook County officials knew about Cavanaugh’s tax or licensing problems in Indiana when he was hired in October 2016 to be Arunkumar’s chief deputy at a salary of $250,000. He couldn’t start work until state regulators issued him an Illinois medical license in February 2017.

After five months, Arunkumar demoted Cavanaugh to assistant medical examiner — the job he had when the medical examiner says her staff discovered errors in his reports last October. He was fired Nov. 30.

Cook County medical examiner's office.

The Cook County medical examiner’s office is reviewing each of the 218 cases that Dr. John E. Cavanaugh handled. | Sun-Times files