James Holmes, 24, sat in court in a red jail suit with dyed orange hair, and appeared sleepy during the proceedings.
Nine of 58 people wounded by the gunman remain in critical condition.
On Sunday, President Barack Obama met survivors and families of the dead as hundreds of people took part in a service of remembrance.
James Holmes is to be held without bail at a jail in Centennial, Colorado, the judge said.
He is accused of throwing two canisters of gas into a busy midnight screening of The Dark Knight Rises before firing at random at the crowd. Witnesses say he was wearing full body armour during the attack.
It is reported that a semi-automatic rifle jammed during the attack and the gunman switched to a weapon with less firepower, possibly saving some lives.
James Holmes was being held in solitary confinement. Police say he is not co-operating with them.
The dead include a six-year-old girl and two US military servicemen.
James Holmes appeared in court at 09:30 local time for the first stage in a process likely to see him face at least 12 counts of first-degree murder. He could face further charges of aggravated assault and weapons violations.
Prosecutors are to formally file charges on 30 July.
One prosecutor has warned it could take at least a year before James Holmes stands trial, the AP reported.
The office of prosecutor Carol Chambers is considering whether to press for the death penalty for James Holmes, a decision that will be made in consultation with the victims’ families, she said.
On Monday morning uniformed police were stationed outside the court house, and deputies were patrolling the roofs of court buildings.
President Barack Obama said that when he visited Aurora on Sunday he had shared hugs and tears, but also laughter as the families recounted the lives of their loved ones.
He added that he visited as much as a father and husband as a president, and that Aurora was in the nation’s thoughts.
Barack Obama said: “I confessed to them words were inadequate but my main task was to serve as a representative of the entire country and say we are thinking about them at this moment each and every day.”
Both President Barack Obama and his Republican Party challenger, Mitt Romney, curtailed their election campaigns in the wake of the Aurora attack, dropping advertising in Colorado state out of respect for victims and their families.
Meanwhile, residents have been laying flowers at a memorial site near the Century cinema and thousands of people have been participating in vigils outside City Hall.
Aurora Mayor Steve Hogan told the crowd on Sunday: “While our hearts are broken, our community is not.”
On Saturday police managed to gain access to James Holmes’ flat, which had been laid with booby traps connected to explosives that could have killed someone entering through the door.
The FBI is now collecting evidence, and investigators say a computer found inside his home could provide crucial details.
Several US media outlets have reported that a Batman mask and poster were in the flat, but police have not confirmed this.
Police said the suspect had acted with “calculation and deliberation”, adding that he had been stockpiling ammunition for months.
Over the course of eight weeks he bought 6,300 rounds of ammunition: 3,000 for a .233 semi-automatic AR-15 rifle, 3,000 for two .40 Glock 22 pistols and 300 cartridges for a pump-action shotgun.
James Holmes bought the four weapons legally.
Authorities say the suspect is not linked to terror groups and have not established a motive for the attack. James Holmes had no criminal record other than a speeding fine.
James Holmes grew up in San Diego and was pursuing a PhD in neuroscience at the University of Colorado in Denver. School officials have said that he recently left the programme.
Names of the dead in Aurora cinema shooting:
• Jessica Ghawi, 24
• Veronica Moser, 6
• John Larimer, 27
• Alexander Boik, 18
• Jesse Childress, 29
• Jonathan Blunk, 26
• Rebecca Ann Wingo, 32
• Alex Sullivan, 27
• Gordon Cowden, 51
• Micayla Medek, 23
• Alexander Teves, 24
• Matthew McQuinn, 27 (presumptively identified, awaiting confirmation)
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