A judge in the United States ordered that DNA tests be performed to determine the biological father of Dannielynn. Following Smith's death, Debra Opri, the lawyer for Larry Birkhead, asked for an emergency DNA sample to be taken from her body. Smith's lawyer, Ron Rale objected strongly to this request. The request was denied by a judge, who instead ordered Smith's body preserved until February 20.

According to a story published in the New York Daily News, Donna Hogan, Smith's younger half-sister, has said that the model froze the sperm of her second husband, Marshall, prior to his death. The newspaper said that Hogan wrote in her unpublished manuscript about her sister, entitled Train Wreck, that "To her family, she hinted that she had used the old man's frozen sperm, and would be giving birth to Howard Marshall's child".[dead link] However, the publisher of Hogan's book described the newspaper's claims as a hoax. On February 9, 2007, Zsa Zsa Gabor's husband Frédéric Prinz von Anhalt said that he had had a decade-long affair with Smith and could potentially be the father of her infant girl, Dannielynn. Alexander Denk, a former bodyguard for Anna Nicole Smith, reportedly told the tabloid television program Extra that he had had an affair with his former employer, and that it was possible he could be Dannielynn's father.[dead link]

After Smith's death, TMZ.com reported that Smith had been given a prescription for methadone under a false name while she was in her eighth month of pregnancy. The Medical Board of California launched a review into the matter; the prescribing doctor, Sandeep Kapoor, said his treatment was "sound and appropriate."[dead link]

On April 10, 2007, a Bahamian judge ruled Larry Birkhead, a former boyfriend, as the father of Dannielynn. DNA tests had established Birkhead as the father, with 99.99% certainty. Commenting on the revelation, Birkhead stated, "I hate to be the one to tell you this but, I told you so. I'm the father...My baby's going to be coming home pretty soon." Birkhead subsequently applied for an amended birth certificate listing him as the father, which paved the way for him to obtain a passport for the baby and him to leave for the United States. Howard K. Stern did not contest the DNA results or the ruling. Subsequent to the ruling, Birkhead returned to the United States with the baby. Virgie Arthur's appeal of the ruling was later denied and she was ordered to pay costs.

Smith's 20-year-old son, Daniel Smith, died on September 10, 2006 in his mother's hospital room while visiting her and his newborn sister. After the coroner labeled the death "reserved," Smith hired forensic pathologist Cyril Wecht to perform a second autopsy.

His death certificate was issued on September 21, 2006, so that he could be buried. While Smith remained in the Bahamas with Dannielynn and Stern, Daniel's family in the United States, including his father, Billy Smith, gathered with friends on October 7, 2006, in Mexia, Texas, for a memorial service. Daniel was buried at Lake View Cemetery on New Providence, Bahamas, on October 19, 2006, almost six weeks after his death.[dead link] According to Howard K. Stern, Smith's longtime companion, she was devastated over her son's death. "Anna and Daniel were inseparable. Daniel was without question the most important person in Anna’s life," Stern told Circuit Judge Larry Seidlin during his testimony in the legal battle after the model’s death. "At Daniel’s funeral, she had them open the coffin and tried to climb inside. She said that 'if Daniel has to be buried, I want to be buried with him,'" Stern testified. "She was ready to go down with him." Howard K. Stern revealed that "Anna saw herself as both mother and father to Daniel. From the time I met her, everything was for Daniel. I would say that physically, she died last week, but in a lot of ways, emotionally she died when Daniel died," he added.

Dr. Wecht announced on Larry King Live that the autopsy he performed showed that Daniel died from a lethal combination of Zoloft, Lexapro and methadone. Although he explained that methadone is used in the treatment of heroin and morphine addiction, Wecht said he had no information to make any conclusion why Daniel was using the drug. On February 8, 2007, Wecht said on Fox News that he still had no information about how Daniel obtained methadone.

On September 28, 2006, Smith and Howard K. Stern exchanged vows and rings in an informal commitment ceremony aboard the 41-foot catamaran Margaritaville off the coast of the Bahamas. She wore a white dress and carried a bouquet of red roses, while he wore a black suit with white shirt. Although they pledged their love and made a commitment to be there for one another before a Baptist minister, no marriage certificate was issued and the ceremony is not legally binding.

After the ceremony, they landed on the island of Sandy Kay where they had a party and celebrated with champagne and apple cider that had been brought over for the occasion by sailboat.