Delivering the verdict, Special Maharashtra Control of Organised Crime Act (MCOCA) Judge Yatin D Shinde held 12 of the 13 accused guilty, while acquitting one of them.
The convicts were allegedly linked to the banned outfit, Students Islamic Movement of India (Simi).
The accused were found guilty of charges under IPC, Explosives Act, Unlawful Activities Prevention Act, Prevention of Damage to Public Property Act and Indian Railway Act and those under MCOCA.
Five of the accused were found guilty of murder. The court also found all the 12 accused guilty under Section 3 (1) (i) of MCOCA, which could attract capital punishment.
During the investigations, 13 accused, all of them Indians, were arrested and brought to trial. The charge sheet filed by the Anti Terrorism Squad (ATS) in November 2006 had named 30, 17 of them absconding, of which 13 are said to be Pakistan nationals.
Arguments for the quantum of sentence are likely to begin on Monday.
The ATS chargesheet had said improvised explosive devices (IEDs) were made in a room in Govandi in suburban Mumbai and some Pakistani nationals were also present during the bomb-making.
Seven bombs had exploded in the first class coaches in many suburban trains on July 11, 2006, killing 188 people and injuring 829.
In the trial that ran for eight years, the prosecution examined 192 witnesses, including eight Indian Police Service, five Indian Administrative Service (IAS) officers and 18 doctors. The defence lawyers examined 51 witnesses and one person was called as a court witness.
The blast occurred within a span of 10 minutes between Khar Road-Santacruz, Bandra-Khar Road, Jogeshwari-Mahim Junction, Mira Road- Bhayander, Matunga- Mahim Junction and Borivali.
The MCOCA judge had concluded the trial on August 19 last year. The examination of witnesses resumed after two years since the Supreme Court had stayed the trial in 2008.
Before the stay, the prosecution had already examined a police officer. The Supreme Court vacated the stay on April 23, 2010.
Of the 13 accused arrested by ATS between July 20, 2006 and October 3, 2006, 11 had given statements admitting to their involvement in the blasts but later retracted.
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