Protesters shouted "thief" and "fraud" at the former economy minister and deputy prime minister as he arrived at the courthouse outside Madrid.
Rato is standing trial with 64 other former executives and board members at Caja Madrid and Bankia, whose near-collapse sparked an EU bailout of Spain's financial sector.
Rato, 67, entered the courthouse without saying a word for the trial, which is expected to last until December.
It is also another thorn in the PP's side after repeated failed attempts to form a government following two inconclusive elections, due to a lack of support that is in large part due to corruption scandals sullying the party.
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Rato, who led the International Monetary Fund from 2004 to 2007, and the other executives are accused of having paid for personal expenses with credit cards put at their disposal by both Caja Madrid and Bankia, without ever justifying them or declaring them to tax authorities.
According to the indictment, Rato maintained the "corrupt system" established by his predecessor Miguel Blesa when he took the reins of Caja Madrid in 2010.
He replicated the system when he took charge of Bankia, a group born in 2011 out of the merger of Caja Madrid with six other savings banks, prosecutors say.
With his undeclared credit card, Rato is accused of having spent 99,000 euros in two years on items such as luxury bags, five-star hotels and alcohol.
Rato has denied any wrongdoing and said the credit cards were for discretionary spending as part of the pay deal for executives.
During Rato's career as a banker Spain was rocked by another banking scandal considered the country's biggest ever.
Thousands of small-scale investors lost their money after they were persuaded to convert their savings to shares ahead of the flotation of Bankia in 2011, with Rato at the reins.