Judge Garzon accused 12 members of Argentina's former military government of genocide, torture and terrorism during the 1976-83 dictatorship. More than 80 other military officers are charged in a 300-page indictment based on testimony from thousands of victims and their families.
Judge Garzon, who wants General Pinochet to face trial in Spain for abuses during the Chilean dictatorship, plans also to seek the extradition of the Argentines. But such a request is likely to be rebuffed by the Argentine authorities.
Among the 98 charged in the indictment are the former military president, Leopoldo Galtieri, the leader of the 1976 coup, Jorge Videla, and former navy chief Emilio Massera.
To a far greater extent than in Chile, Argentina used "disappearances" as a weapon against political opponents. Human rights organisations who asked Judge Garzon to bring the charges and helped build the case say the military were responsible for 30,000 deaths and disappearances. Official estimates put the number at 15,000.
The disappearances led to the "Mothers of the Plaza de Mayo" - women who marched outside the presidential palace in Buenos Aires each Thursday chanting "Donde Estan?" - where are they?
The military authorities also "disappeared" - kidnapped - babies born to detainees in the prisons and torture centres. Many were adopted by officers' families and given new identities. Some were later reunited with their grandparents who tracked down the offspring of their dead children.
Judge Garzon's Argentine initiative is likely to cause even more diplomatic turbulence than his Pinochet efforts. The outgoing Argentine President, Carlos Menem, has refused to co-operate with the judge's investigation into the fate of several hundred Spaniards during the dictatorship.
Argentina, unusually, put its former military leaders on trial after democracy was restored in 1983. They were sentenced to life in prison, but President Menem - himself imprisoned during the dictatorship - later pardoned and released them.