The baby boy lived only 90 minutes after he was born on Oct. 23, 2003. Without money to bury him, his mother, Katrina DeJesus, reluctantly signed papers letting New York City lay him to rest. She would not be allowed to visit the city cemetery where the baby was buried, officials told her, because it was off limits, under the jurisdiction of the Correction Department.

Twelve years passed. Every year on the birthday of the baby she had named Anthony, she and her living children would cut a cake in his memory, and add a trinket to the small shrine she kept beside her only photograph of him.

Then Ms. DeJesus learned that a lawsuit by other families had opened the way for a visit to the grave site. After calls to a hospital and two city agencies, she was able to sign up for one of the monthly ferry trips now allowed to relatives of those buried in the cemetery, or potter’s field, on Hart Island.

But on the ferry in March, surrounded by her children, she listened as Capt. Martin Thompson of the Correction Department broke inexplicable news: “I’m very sorry to tell you that we have no record of your son.”

Somehow, it seems, the city lost her baby’s body.

“I just broke down, because I thought this whole time that my son was buried, at peace,” Ms. DeJesus, 36, said in an interview last week. “I tried to speak to the captain, but it was too hard for me.”

“Where is my son, then?” she asked. “What have they done with his body?”

Now Ms. DeJesus is suing the city for negligence in destroying her sepulcher rights — the age-old right to bury one’s relatives.

Her lawyer, Daniel Flanzig, filed a formal notice of the claim against the city last week, citing $5 million in damages and naming as defendants the office of the chief medical examiner, the Bronx County medical examiner, the city’s Health and Hospitals Corporation, and the Correction Department.

“The law recognizes the right of kin to find solace and comfort in the ritual of burial,” Mr. Flanzig said, “and the courts have recognized that damages can be assessed against anyone who interferes with that right.”

The belated discovery that the baby’s body was missing echoes more recent problems with corpses lost or mixed up, both in funeral homes and at city morgues. In 2014, the city dug up 274 bodies on Hart Island in a fruitless search for the body of a woman named Rebecca Alper, 71, after a relative asked about her remains. It turned out that she had been wrongly transferred by the city morgue to a funeral home under another woman’s name, and cremated. The mistake and its cover-up came to light nine months later, after the body of the other woman, Leah Lerner, 95, was discovered, languishing in the city morgue.

Julie Bolcer, a spokeswoman for the office of the chief medical examiner, said procedures had changed.

“In the past two years, O.C.M.E. has completed a comprehensive review of its mortuary operations and implemented numerous measures to ensure rigorous quality control and accuracy in service to all families,” she wrote in an email.

Neither Ms. Bolcer nor a spokeswoman for the Correction Department, Eve Kessler, would discuss the case of Ms. DeJesus’ baby because it involves a lawsuit. But Ms. Kessler wrote in an email that the agency considers the administration of the city cemetery on Hart Island “a solemn responsibility.”

Ms. DeJesus said that while she and the children waited on Hart Island at the unmarked grave of other babies, Captain Thompson directed a records search under every combination of her son’s name: Anthony Lerry Then Jr., after his father’s name, as well as “baby boy DeJesus.” Later, the medical examiner’s office told her that it had found a record of her baby’s body being checked in at the Bronx morgue, she said, but no record of it being checked out again for transport to Hart Island. The lawsuit will push for more disclosure.

Every day, her children, 15, 9 and 6, ask whether their brother has been found, she said. She tells them, “We got to keep fighting.”

Meanwhile, painful memories are vivid again.

The baby was one month premature, and had congenital disorders of the lungs and kidneys that made his survival impossible, according to an autopsy conducted the day after his death at St. Barnabas Hospital in the Bronx. The hospital gave her one week to claim the body.

“I was trying my best to find the money,” Ms. DeJesus recalled of her inquiries at funeral homes and her futile efforts to borrow the sums they required. “People told me, ‘Go to welfare, they will help you with the money to bury your son.’ But they didn’t. They just turned their back on me,” she said of caseworkers at her local public assistance office, who said they could not grant her money to bury her son.

So she went back to the hospital and signed her baby’s body over to the city. She asked if she could see him one last time. In the refrigerated hospital morgue, an attendant opened the blanket that her baby was wrapped in. “It hurt me to see him like that,” she said.

“I put my child’s body in their hands to bury him, to be at peace, and they didn’t commit to it,” she added. “To have me trusting the city and trusting everybody to make sure that my baby was at peace, and for them to come to me now and say they don’t know where my baby is. How can I possibly live with that?”