Khodorkovsky is charged with embezzling more than $25 billion worth of oil and laundering most of the proceeds, charges his lawyers say are ridiculous.
The legal assault on Khodorkovsky and his business partners, which dates back to 2003, is widely seen as punishment for challenging Vladimir Putin, the former Russian president who remains as powerful as ever in his current role as prime minister.
Khodorkovsky's defense lawyers contend that prosecutors have produced no evidence to support the charges, which they say rest on allegations that Khodorkovsky and his partner Platon Lebedev embezzled all of the crude produced by their Yukos oil company from 1998 to 2003.
Prosecutors have failed to explain how the company could have covered its expenses and expanded production if all the oil it had was being stolen, the defense lawyers contend.
Lebedev, who spoke first Tuesday, said the trial was "rotten" and demanded the removal of the judge.
The judge called two recesses: one after Lebedev's outburst and another after Khodorkovsky's call for the case to be dismissed. It was unclear whether either defendant would be allowed to speak again Tuesday.
The trial is considered a test of whether President Dmitry Medvedev, himself a lawyer, is serious about reforming Russia's troubled judicial system.