Khodorkovsky, Russia's richest man, will be tried along with another YUKOS major shareholder Platon Lebedev.
The trial is seen by many as a government-inspired campaign to jail Khodorkovsky and strip him of his wealth.
His downfall is said by analysts to be the work of people in the Kremlin who fear he was using his wealth to sway public policy and mount a challenge to their authority.
Khodorkovsky, 40, wearing a brown leather jacket, arrived in a large blue van at a side entrance to the Meschchansky district court in Moscow and was led in by police.
Inside the building, he waved to his parents, reporters and lawyers before being taken into the courtroom.
The trial, before a panel of three judges, is an important test case for President Vladimir Putin, who has said he wants justice to run its course in the YUKOS affair. He has also warned tax evasion will not be tolerated and other captains of industry may face prosecution.
Human rights activists accuse Putin of manipulating the judicial process to suit the state's interests.
Wednesday's hearing is part of a two-pronged judicial assault on YUKOS and its owners which comes to a head this week and could pitch the company into bankruptcy.
"They are going to be found guilty. We know the outcome"
A Moscow court will hear an appeal on Friday by Russia's tax ministry aimed at forcing YUKOS to pay a $3.4 billion bill for back taxes immediately.
If the court finds in favour of the tax authorities, as expected, YUKOS says it may go bust because another court has frozen the company's assets, making it impossible for YUKOS to raise enough cash in time to pay the bill.
A member of Khodorkovsky's legal team said he was in little doubt both men would be convicted and receive jail sentences of up to 10 years.
A Toronto-based lawyer, Robert Amsterdam said, "They are going to be found guilty. We know the outcome. It is a show trial to help the government expropriate YUKOS."
Some analysts believe that if YUKOS is driven out of business, Khodorkovsky and his associates, who control the oil group through a company called Menatep, will be dispossessed of
their prize asset.
Human rights activists accuse
Putin of manipulating judiciary
The trial is the most prominent of a business figure since the fall of the Soviet Union in 1991. Khodorkovsky has been held in pre-trial detention since his arrest in October and Lebedev
since last July.
Some western lawyers say Lebedev and Khodorkovsky, accused of making liberal use of offshore financial havens to conceal profits and minimise tax payments, may have a case to answer.
The two face seven criminal charges, including one of fraudulently obtaining shares in Apatit, a fertiliser firm which was privatised in 1994
Lawyers, acting for Khodorkovsky and Lebedev, say the defendants acted within the law.
Amsterdam said he believed the trial could be adjourned for a number of days to enable a member of the defence team to recover from medical treatment.