The Will County Sheriff's Office said in a news release that a lawyer for Dr Ulrich Klopfer's family contacted the coroner's office on Thursday about possible foetal remains being found at the home in an unincorporated part of Will County in northeastern Illinois.
The sheriff's office said authorities found 2,246 preserved foetal remains, but there's no evidence medical procedures were performed at the home.
The coroner's office took possession of the remains. An investigation is under way.
Dr Klopfer, who died on September 3, was a long-time doctor at an abortion clinic in South Bend, Indiana.
It closed after the state revoked the clinic's licence in 2015. The Indiana State Department of Health had previously issued complaints against the clinic, accusing it of lacking a registry of patients, policies regarding medical abortion, and a governing body to determine policies.
The state agency also accused the clinic of failing to document that patients get state-mandated education at least 18 hours before an abortion.
Dr Klopfer was believed to be Indiana's most prolific abortion doctor, with thousands of procedures performed in multiple Indiana counties over several decades, the South Bend Tribune reported.
Christian, Mike Fichter, the president of the group Indiana Right to Life, said in a statement that "we are horrified" by the discovery of the foetal remains at Dr Klopfer's Illinois residence.
He called for Indiana authorities to help determine whether those remains have any connection to abortion operations in Indiana.
"These sickening reports underscore why the abortion industry must be held to the highest scrutiny," Mr Fichter said in the statement.
Dr Klopfer's licence was suspended by Indiana's Medical Licensing Board in November 2016 after the panel found a number of violations, including a failure to ensure that qualified staff was present when patients received or recovered from medications given before and during abortion procedures.
Dr Klopfer was no longer practising by that time, but he told the panel he had never lost a patient in 43 years of doing abortions and that he hoped to eventually re-open his clinics.
In June 2014, Dr Klopfer was charged in St Joseph County, Indiana, for failure to file a timely public report.
He was accused of waiting months to report an abortion he provided to a 13-year-old girl in South Bend.
That charge was later dropped after Dr Klopfer completed a pre-trial diversion programme.
Republican US Representative Jackie Walorski called the discovery of the foetal remains "sickening beyond words" in a statement released by her office.
"He was responsible for thousands of abortions in Indiana, and his careless treatment of human remains is an outrage," she said in her statement.
In May, the US Supreme Court upheld an Indiana law requiring the burial or cremation of foetal remains following abortions in the state.
That law was signed by Vice President Mike Pence in 2016 when he was Indiana's governor, but it was the subject of legal challenges.
The Indiana State Department of Health, which oversees abortion clinic regulation, has integrated that law's provisions into the agency's existing licensing process.
Prior to the ruling, Indiana clinics could turn over foetal remains to processors who handle the disposal of human tissues or other medical material by incineration.
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