The newborn sister of AJ Freund, the five-year-old Illinois boy whose parents reported him missing before his body was found buried in a shallow grave in April, has been taken into protective custody pending the results of paternity tests.

AJ's mother, JoAnn Cunningham, 36, delivered her daughter on May 31 in jail while awaiting trial for her son's killing.

Both she and her ex-boyfriend, AJ's father Andrew Freund Sr, 60, remain behind bars in connection to their son's disappearance and death in April.

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JoAnn Cunningham, 36, gave birth to a daughter on May 31 while in jail awaiting trial for the murder of her five-year-old son, AJ Freund

Who's the father? It is unclear whether the baby girl was fathered by Cunningham's ex-boyfriend Andrew Freund Sr, 60 (left), or her subsequent paramour Daniel Nowicki, 36 (right)

Cunningham was reportedly permitted to spend two days with her baby daughter in the hospital before the newborn was taken away by the state Department of Children and Family Services, according to CBS Chicago.

The child will remain in state custody until the question of her paternity is settled.

It is unclear whether Freund Sr, or Cunningham's subsequent boyfriend, 36-year-old Daniel Nowicki, is the baby girl's biological father, reported Northwest Herald.

Last month, a judge ordered both men to undergo paternity tests, the results of which are expected to come back on August 12.

Cunningham and Freund's five-year-old son, AJ (pictured), was found buried in a shallow grave in April, a week after his parents filed a false missing person report

Nowicki said after the June 10 hearing he believes he is the girl's father.

Nowicki was arrested the following day for violating his plea agreement in connection to a December 2018 incident involving aggravated battery on a hospital guard and two nurses. He is due back in court in that case on Wednesday.

Cunningham and Freund's other son is also currently in state custody. Prosecutors have previously asked to have the couple's parental rights stripped over AJ's younger brother.

A separate petition would have to be filed seeking to have Cunningham's parental rights revoked over her baby daughter.

Cunningham pleaded not guilty last month to first-degree murder, aggravated battery, aggravated domestic battery and failure to report a missing or child death.

Freund pleaded not guilty to the same charges, as well as additional counts of concealment of a homicidal death.

Cunningham and Freund reported AJ missing from their filthy, feces-smeared Crystal Lake, Illinois, home, on April 18, three days after he died.

Cunningham was seven months pregnant with her daughter at the time.

Cunningham was seven months pregnant when in April she called on the public to help find her missing son, AJ

A week later, police found AJ's plastic-wrapped body buried in a shallow grave in a field in nearby Woodstock.

According to an affidavit, the parents forced AJ to take a 20-minute cold shower on April 14 as punishment for lying about soiling his underwear.

Freund told investigators they put the boy to bed 'cold, wet and naked' and Cunningham later found him unresponsive.

Freund said he put AJ’s body in a plastic container and stored it in the basement before later burying him. An autopsy found AJ died from multiple blunt force injuries to his head.

Investigators say that the Department of Child and Family Services had visited the Freund home 17 times over the last five years.

In those visits, authorities described the squalid condition of the home, the apparent drug use of the parents who are 'known and self-admitted prior narcotics abusers' and concern for the welfare of AJ and his four-year-old brother, Parker.

Police said the home was found to be in 'hoarder-like condition' with garbage bags of 'wet refuse' stacked in the basement and garbage area.