Spain's top National Court launched proceedings in a lawsuit brought against Rato for alleged fraud in his role as chairman of Bankia, from which he resigned in May just before the lender was bailed out, court documents showed.
The 23.5 billion euro ($29.5 billion) bailout announced by the Spanish government for the lender on May 9 marked a new phase in Spain's banking crisis, driving it to seek eurozone rescue funds for its finance sector.
The court accepted a suit brought by UPyD, a centrist opposition political party, targeting Rato and 32 other senior members of the bank as well as its mother company BFA.
Court papers seen by AFP listed the charges of crimes including fraud, embezzlement, falsifying accounts and price manipulation.
No date was set for hearings in the case.
Anti-corruption judges had already opened a preliminary investigation into alleged fraud relating to Bankia's founding and stock listing, which took place in 2010. The entity was created by merging seven regional savings banks.
Rato is one of the most prominent financial figures in Spain, having served as economy minister from 1996 to 2004 and then as managing director of the IMF until 2007.
Trying to stamp out fears of a general banking collapse, Spain's conservative government nationalised Bankia, formerly its fourth-largest listed bank, taking a 45-percent stake by converting loans into shares.
On June 9, the eurozone agreed to extend a credit line of up to 100 billion euros to stabilise Spain's banks, amid fears for the country's financial health, gravely weakened by the collapse of a property boom in 2008.
Eurozone finance ministers are due to discuss exactly how much of this amount Spain will borrow at a meeting on July 9.
The lawsuit by UPyD was one of four cases brought by diverse bodies including the far-right organisation Manos Limpias and two social protest groups, Democracia Real Ya and a movement popularly known as the "indignants".
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