Earlier, ATS had said that Jundal was involved in terror activities from 1996.
Jundal, however, pleaded innocent before the court.
When the charges were read out to him, Jundal denied all of them and even said that he had never been a part of banned organisations SIMI or LeT.
Meanwhile, Jundal's lawyer filed an application in the court that he should not be kept in solitary confinement in the Arthur Road Jail.
On May 8, 2006, a Maharashtra ATS team chased a Tata Sumo and an Indica car on Chandwad-Manmad highway near Aurangabad and arrested three terror suspects and seized 30kg of RDX, 10 AK-47 assault rifles and 3,200 bullets.
The Indica was allegedly driven by Jundal, who managed to give police the slip and drove to Malegaon. During the same month, he escaped to Bangladesh.