The magazine's report, appearing in the issue that hits newsstands Wednesday, is based on internal documents, e-mails, photographs and tape recordings supplied by a former employee of Alcor Life Extension Foundation.
After Williams died July 5, 2002, his body was taken by private jet to the company in Scottsdale, Ariz. There, Williams' body was separated from his head in a procedure called neuroseparation, according to the magazine.
The operation was completed and Williams' head and body were preserved separately. The head is stored in a steel can filled with liquid nitrogen. It has been shaved, drilled with holes and accidentally cracked 10 times, the magazine said. Williams' body stands upright in a 9-foot tall cylindrical steel tank, also filled with liquid nitrogen.
The procedure, approved by Williams' son, John Henry, and daughter, Claudia, carries a $136,000 bill. Alcor claims it is still owed $111,000.
Williams' eldest daughter, Bobby-Jo Williams Ferrell had fought against the process, saying that her dad had asked and requested in his will to be cremated and his ashes, scattered off the Florida coast.
Yet Williams' signature, along with John Henry and Claudia's had appeared at the bottom of handwritten note dated more than three years after the baseball star signed a will asking to be cremated.
"JHW, Claudia and Dad all agree to be put into biostasis after we die," reads the pact, which family attorney Bob Goldman said was written in a Gainesville hospital room before the Hall of Fame slugger underwent surgery.
"This is what we want, to be able to be together in the future, even if it is only a chance," the document said.
Sports Illustrated said that according to a taped conversation between former Alcor chief operating officer Larry Johnson and a board adviser, eight DNA samples among 182 taken from Williams are missing without explanation.
Spokeswoman Paula Lemler, wife of Alcor chief executive officer Jerry Lemler, told The Associated Press on Tuesday that company officials had not seen the article and would have no comment.