The charges stem from alleged torture at Villa Grimaldi, a secret detention center where Michelle Bachelet, now president of Chile, once was detained, along with other political prisoners.
Pinochet on Friday was charged with the torture and disappearances of people in state custody who opposed his 1973-1990 rule.
Judge Alejandro Solis charged last week that Pinochet was responsible in 36 cases of "forced disappearances," a murder and 23 cases of torture committed in the jail.
Pinochet, 90, already has lost the immunity he enjoys as a former de facto ruler of Chile on several occasions, but has never stood trial for any of the 3,000 deaths and torture committed, according to an official count.
The former dictator, who ruled with an iron fist between 1973 and 1990, is also under investigation for alleged tax evasion and fraud following the discovery of previously undeclared bank accounts in the United States.
Villa Grimaldi, the name given a former mansion in Santiago was a torture center from 1973 until 1978 run by Pinochet's feared secret police, DINA.
Bachelet and her mother, Angela Jeria, were imprisoned there and tortured for a month in 1975 after the arrest of Bachelet's father, air force general Alberto Bachelet.
Chile's military toppled elected Socialist president Salvador Allende in 1973.
Meanwhile, another Chilean judge vowed on Friday to probe the authenticity of documents showing Pinochet had stashed nine tonnes of gold in Hong Kong at HSBC bank, despite the British banking giant's insistence that the documents are false.
The documents say Pinochet's deposit was worth 160 million dollars. Other sources said the deposit would be worth 190 million dollars in today's market.

Copyright AFP (Agence France-Presse), 2006