It is the first time in Peru's history that a former president has faced a public trial for crimes committed during his rule.
In November 2000, Fujimori had ordered an aide to break into a house where Vladimiro Montesinos, the intelligence chief, had hidden dozens of boxes of videos and tapes documenting government corruption.
In the human rights trial that began on Monday, Fujimori is accused of ordering two massacres that killed 25 people and two kidnappings when Peru was battling Maoist fighters.
Fujimori on Monday denied being involved in any of the killings and angrily protested his innocence, saying he "never ordered the death of anybody".
A three-judge Supreme Court panel is reviewing charges that he authorised an army death squad to identify and kill suspected Maoist Shining Path guerrillas and collaborators.
A truth and reconciliation commission found that none of the victims were connected to the Shining Path, which had carried out an armed campaign against the government.
The trial will also seek to determine if Fujimori ordered or knew about the kidnapping and detention of a journalist and businessman critical of his government, as alleged by a former operations chief of the La Colina death squad.
The prosecution has called for a 30-year jail sentence and the payment of more than $33m in damages.
In later trials, Fujimori is expected to face allegations that he illegally used $15m in state money to pay Montesinos to resign.
He is also accused of authorising bribes to congressmen and illegal phone taps, and that he secretly bought a TV station for political propaganda using state funds.
Fujimori initially received widespread support for his crackdown on the guerrillas and his economic reforms, which ended hyperinflation inherited from the previous government and spurred record foreign investment.
But his government became increasingly authoritarian, intimidating the media, human rights groups and political parties.
In November 2000, Fujimori, fled to Japan amid a bribery scandal that forced him from power.