The appearance marks the first time the Shiite leader would be tried in public since his arrest and detention in December 2015.
The State Security Service, SSS, has held the Shiite leader in detention despite a court order ordering his release.
He was arrested following a clampdown on his supporters who blocked the army chief, Tukur Buratai, from using a public road.
Over 340 members of the Shiite group were killed by the soldiers in attacks condemned by local and international rights groups.
One soldier was also killed.
While no soldier is being prosecuted for the mass killings of the Shiites, the Kaduna government is prosecuting Mr El-Zakzaky for the death of the soldier.
It is for that trial that Mr El-Zakzaky was brought to court on Tuesday.
LETS TALKBLOG learnt that Mr El-Zakzaky and his wife, Zeenah, were brought to court at about 9:00a.m.
They were said to have been brought into Kaduna the previous night from where he was kept.
Persons who were not staff of the High Court were also turned away from the area.
The counsel to Mr El-Zakzaky, Maxwell Kyom, told LETS TALKBLOG that the cleric is being charged with unlawful gathering, criminal conspiracy and culpable homicide punishable with death.
Mr Kyom said the case could not continue because two of the defendants were not in court.
According to him, an oral application was moved for the bail of the cleric and his wife. But the presiding judge, Gideon Kurada, asked him to put his application officially in writing.
The case was adjourned to June 21 by the presiding judge based on application by the prosecutor for them to properly file their statement of claim.
Following the trial, IMN members protested in Kaduna demanding the release of their leader.
A member of the group, Abdulhameed Bello, said they were disappointed with the trial because the federal government refused to heed an earlier court ruling granting bail to the cleric.
“We call on the Federal and Kaduna State Governments to as a matter of urgency obey the judgment of the Abuja court and release the Sheikh for peace to reign,” he said.
Mr Bello explained that IMN members will continue to use all peaceful means to put pressure on the government to release the detained cleric.