17 persons were killed and over 50 injured in the blast at the German Bakery, a popular eatery in Pune`s posh Koregaon Park area, on February 13, 2010.
Additional District and Sessions judge N P Dhote framed the charges under various sections of IPC, including 302 (murder), 307 (attempt to murder), 120 (b) (criminal conspiracy) along with relevant sections of Unlawful Activities (Prevention) Act and Explosives Substances Act.
Baig, who hails from Udgir in Marathwada region of Maharashtra, is also charged with promoting enmity between two groups and "mischief by fire or explosive substance" under the Indian Penal Code.
Maharashtra Anti-Terrorism Squad had filed the charge sheet against Baig and six absconding accused on December 4, 2010.
Baig (29) denied the charges when the judge read them out to him in Hindi.
Public prosecutor Raja Thakre told the court that he would be submitting additional forensic evidence in the case, on which the judge asked defence counsel A Rehman to file his say.
The defence counsel filed an application before the court saying Baig was suffering from typhoid and should be examined in a private hospital. The plea was granted by the court.
Next hearing of the case is on July 30.