Prosecutors said the disgraced money manager will face up to 150 years in prison on the charges.
The details of the criminal case emerged at a hearing Tuesday to resolve several potential conflicts of interest between Madoff and his lawyer, Ira Sorkin.
Sorkin and his family invested more than $900,000 with Madoff. After questioning Madoff, the judge ruled that Sorkin may continue representing Madoff.
Asked by the judge if Madoff would plead guilty Thursday, Sorkin said: "I think that's a fair expectation."
Madoff wore a bulletproof vest as he entered the courthouse - his first public appearance after nearly a month of seclusion in his luxury Manhattan apartment.
The 70-year-old former Nasdaq chairman has been under house arrest since he was charged in December with swindling investors out of billions of dollars. He last appeared in court on Jan. 14.
The hearing Tuesday was a precursor for another highly anticipated proceeding Thursday, when Madoff isin perhaps the largest securities fraud case in history.
And on Monday, the Wall Street Journal reported that one of Madoff's top aides directed employees to generate fake trading tickets to dupe clients into thinking their imaginary returns were legitimate.
At least 25 Madoff investors have asked to speak Thursday under oft-overlooked provisions allowing victims of crime to appear at a defendant's plea hearing.
Attorney Jerry Reisman, who represents more than a dozen Madoff investors, predicted that Thursday's hearing would be "a zoo."
"I will tell you my clients are outraged by his being able to escape with a guilty plea," he said.
Although Tuesday's hearing was expected to be largely procedural, the courthouse was using it as a dry run for Thursday, showing the proceedings on a large screen in a second courtroom and in the juror assembly room, which can fit hundreds of people.
In papers filed Tuesday, prosecutors for the first time detailed the financial ties between Madoff and Sorkin. They said Madoff should be asked to voluntarily waive his right to conflict-free representation.
The investments "could put Mr. Sorkin in a position where his loyalties are divided between Mr. Madoff on the one hand, and his sons and their financial interest on the other," prosecutors wrote. "The government believes, however, that any potential conflict arising out of the financial interests of Mr. Sorkin's sons is waivable."
The papers said Sorkin's parents had invested approximately $900,000 with Madoff to create trust accounts for Sorkin's two sons. They said Sorkin has told the government that he is a trustee of the sons' trust accounts but has never had a beneficial interest in the money.
Prosecutors also noted that Sorkin once invested $18,860 with Madoff through a retirement account in the early 1990s. They said, however, that they did not believe this represented a conflict because it was liquidated more than a decade ago.
The government said it also believes Madoff can waive any potential conflict of interest caused by Sorkin's prior representation of two potential witnesses in the case, Frank Avellino and Michael Bienes.
The government said the pair's accounting firm, Avellion & Bienes, was dissolved after it settled accusations in 1993 by the Securities and Exchange Commission that it had sold unregistered securities and operated as an unregistered investment company from 1962 to 1992.
Prosecutors said Madoff has had a long-standing business relationship with Avellino and Bienes and that money Avellino and Bienes raised from their clients was invested with Madoff.