He and his sons Alaa and Gamal also denied corruption charges against them.
After a four-hour hearing -- Mubarak's first public appearance since he resigned on February 11 -- the trial of the father and sons was adjourned until August 15.
Former interior minister Habib al-Adly and six of his deputies were also in the dock, but they are due in court again on Thursday.
Judge Ahmed Refaat, presiding over the Cairo Criminal Court, said Mubarak would be held at the International Medical Centre, a hospital on the outskirts of Cairo, until the next hearing.
In response to a request by the defence team, he agreed to allow an oncologist to monitor Mubarak's health during his hospital stay.
Alaa and Gamal seemed composed throughout the hearing and appeared to take turns shielding their father from the television cameras, leaning over regularly to talk to him.
The trial of Mubarak, whose spectacular downfall sent shock waves across the Middle East and North Africa, was a key demand of the uprising.
The Muslim Brotherhood, which was banned under Mubarak and formed the Freedom and Justice Party after his ouster, hailed the trial as "a real victory for the will of the people."
"The fact that millions could watch the trial on television screens will reassure the Egyptian people that justice is on the right course," said FJP secretary general Saad Katatni.
"If things continue in this way, it will build the bridges of trust between the people and the ruling body in Egypt during this phase," Katatni said.
And political commentator Gamal Fahmy said it is a "rare event not only for Egypt, but for the whole Arab region".
"The most important thing is that it has created a feeling of self-confidence for the Arab peoples who saw with their eyes a ruler being judged by his people," he said.
The United States said it is confident the trial will be fair and transparent.
State Department deputy spokesman Mark Toner said this was important, and "we have confidence that they can do that."
In court, one civil society lawyer called for Field Marshal Hussein Tantawi, head of the ruling Supreme Council of the Armed Forces (SCAF) and Mubarak's long-time defence minister, to testify in the trial.
Lawyers jostled for microphones during the hearing that was for the most part conducted in an orderly manner.
"God gives sovereignty to whom he pleases, and takes away sovereignty from whom he pleases. God glorifies whom he wills, and he humiliates whom he wills," one of the victims' lawyers, quoting the Koran, Islam's holy book, recited to the judge.
Outside the court room clashes erupted between loyalists and foes of the former president, with several people injured.
Pro-Mubarak protesters carried pictures of him, while his opponents held up posters of the former president behind a noose, and security forces stepped in repeatedly to separate both sides.
The crowd, including families of the some 850 people killed during the uprising, had been watching the trial on a large screen outside the police academy -- once called the Mubarak Police Academy.
Until the last minute, it was widely believed Mubarak would not show up, or that the trial would open and then be adjourned indefinitely.
It was an epic downfall, unthinkable just six months ago, a once absolute ruler now a caged invalid.
The hearing has gripped the nation, and Cairo's usually bustling streets were abnormally quiet during the proceedings.
Mubarak, 83, was flown to Cairo from the Red Sea resort of Sharm el-Sheikh where he had been in custody in hospital being treated for a heart condition.
Security was tight, with barbed wire outside the police academy and more than a dozen riot police trucks securing the entrances, an AFP reporter said.
The trial is being held in an auditorium fitted with a large black cage to hold the defendants, including Adly on whom Mubarak relied to quell the revolt, and the six police chiefs.
Businessman Hussein Salem, a close associate of the Mubaraks, is being tried in absentia.
The defendants are accused of stealing millions of dollars from the state and ordering the killing of anti-regime protesters during the uprising.
More than 1,000 police and soldiers secured the complex and vetted some 600 lawyers and journalists.
For weeks, it seemed likely that Mubarak, who doctors say refused to leave his hospital bed, would be tried in Sharm el-Sheikh, but the justice ministry announced last week the trial would be held in Cairo.
His lawyer Farid al-Deeb claimed that Mubarak suffers from cancer and went into a coma last month, which the hospital denied.
One of his doctors told AFP the ex-president was stable, but extremely depressed and weak after refusing food for several days.
Deeb's announcements appear to have been intended to increase sympathy for Mubarak and spare him the indignity of appearing in the defendants' cage.
But the military, which assumed power after Mubarak's resignation, is keen to prove it harbours no lingering loyalties to the former president.
The trial is the latest in a string of legal proceedings against Mubarak-era officials.
Several ministers have already been given jail terms in corruption cases, including Adly, already sentenced to 12 years for graft.
On Tuesday, international rights groups urged a "fair and transparent" trial.
"This trial presents a historic opportunity for Egypt to hold a former leader and his inner circle to account for crimes committed during their rule," said Malcolm Smart, Amnesty International's director for the Middle East and North Africa.
Sarah Leah Whitson, his counterpart at Human Rights Watch, said: "If these proceedings scrupulously reflect the international fair trial standards, it will embody a clean break with the record of impunity that characterised Hosni Mubarak's rule, contribute to a new and hopeful chapter in Egypt's history and SET an important regional precedent."
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