Mr FitzPatrick, former finance director Willie McAteer and former managing director Pat Whelan appeared before the Circuit Court in Dublin yesterday. A provisional trial date has been set for January 2014.
Mr FitzPatrick (64), Mr McAteer (61) and former managing director of lending Mr Whelan (50) face 16 charges of providing unlawful financial assistance to individuals in July 2008 to buy shares in the bank.
The court heard it was a complex case and legal teams needed time for documents to be disclosed, studied and culled.
Brendan Grehan, for Mr McAteer, said the trial could take a minimum of three months. He said 24 million documents would have to be considered as part of the State's investigation, and issues will inevitably arise as part of this.
"It will be considerably more complex than any previous case," he said.
The 16 charges are linked to loans of €451m in an alleged plot involving the family of bankrupt former billionaire Sean Quinn and a golden circle of clients hand-picked to invest in stock to prop up the share price.
All three men were dressed in suits and sat in the public gallery for the short hearing. They did not address the court.
Una Ni Raifeartaigh, prosecuting, told Judge Mary Ellen Ring that the disclosure of evidence to the defence was continuing.
She said it was not simply a question of providing the defence with the documents but that it was necessary to give the defence an opportunity to absorb them and ample time would be needed to examine them.
She asked the court to fix a trial date and appoint a pre-trial judge to deal with any disclosure issues, which may be decided on March 6.
Judge Ring noted that the charges dated to 2008 and the men were sent for trial last October. She told the court that if the disclosure of evidence couldn't be completed in a year then there was something wrong with the system – and set the trial date for January 13, 2014.
"If you can't get it done in 12 months, it says something about the whole of the system," Judge Ring added.
She remanded them on continuing bail on the existing terms and conditions.
Separately, Mr FitzPatrick has been charged with 12 counts of giving auditors false or misleading information on directors' loans totalling almost €140m over a five-year period.
He is due before Dublin District Court for that case in March.
Last week, the High Court extended for another year an investigation by the Director of Corporate Enforcement into the 2008 collapse of Anglo Irish Bank.
The director had sought a three-year extension of orders allowing retention of documents seized from the bank for the investigation.
However, Mr Justice Peter Kelly said he would extend the orders only for one year to January 2014 as he was anxious a three-year extension would not give rise to any reduction in the "intensity" of the probe.