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A federal judge in Manhattan ruled yesterday that Flagstar Bancorp Inc. (NYSE: FBC) must pay $90.1 million to bond insurer Assured Guaranty Ltd. (NYSE: AGO) in a mortgage “putback” case. The amount may be relatively small, but the impact could be startlingly large.

At issue was a claim by Assured that Flagstar had misrepresented the quality of loans the bank packaged into securities and passed on to Assured to guarantee. Loan guarantors, like Assured, have sued to force banks to take back the crappy securities and return the fees that the guarantors paid. Hence the name “putback.”

Assured had sought $116 million from Flagstar for misrepresenting the quality of the loans included in two securitization packages valued at more than $900 million. Assured guaranteed the loans and, when the mortgage crisis hit, the agency had to pay millions of dollars in claims.

This is just the first putback case that has gone to trial. According to a report at Reuters, other suits have been filed by insurers such as MBIA Inc. (NYSE: MBI) and Ambac Financial Group against J.P. Morgan Chase & Co. (NYSE: JPM), Credit Suisse Group A.G. (NYSE: CS) and Bank of America Corp. (NYSE: BAC), among others.

Flagstar had reserved $82.7 million to pay claims for litigation, including the Assured case, and it does not appear that that will be enough. That is what should be making the big banks, particularly Bank of America and its Countrywide Financial unit, quake in their boots.

Flagstar was ordered to pay out 78% of sum sought by Assured. That sets a baseline for putback claims against all banks, and there is absolutely no chance that any bank has reserved anywhere near that amount to pay these claims. And Flagstar was not even charged with fraud, just misrepresentation.

Shares of Bank of America are down about 1% in premarket trading this morning, at $11.76 in a 52-week range of $6.72 to $12.20. The bank is heavily exposed to these claims, and rather than take them to trial, the odds favor some sort of settlement with the insurers. Either way, it will cost BofA and other banks serious money if this ruling is upheld on appeal.