In post-crisis penalties, Morgan Stanley stands alone

August 26, 2013, 1:00 PM UTC

FORTUNE — Nearly five years after the fall of Lehman Brothers, Morgan Stanley has earned some bragging rights. It’s the only major bank that hasn’t paid a federal fine related to the financial crisis.

Morgan Stanley (MS) hasn’t even been accused of breaking the law. Neither have any of its bankers.

On its website, the Securities and Exchange Commission has a list of firms that have paid fines for financial crisis-related crimes. Wells Fargo (WFC) is on the list, as is Goldman Sachs (MS). Bank of America (BAC), Citigroup (C), and JPMorgan Chase (JPM) are all on the list twice. There are also a number of foreign banks, including Credit Suisse (CS), RBC and UBS (UBS), and some smaller firms, like Jefferies, all of which played a minor role in selling mortgage bonds and the financial crisis in general. In all, the SEC has charged 161 firms or individuals, generating $2.7 billion in fines. Morgan Stanley is not on the list.

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Deutsche Bank (DB) is the only firm that comes close to Morgan Stanley’s clean record. It, too, isn’t on the SEC’s list. But Deutsche has been sued by the Justice Department. Last year, the German bank agreed to pay a $202 million fine to settle charges that it deceived the FHA into insuring faulty mortgages.

Morgan Stanley was one of the largest underwriters of mortgage bonds in the run-up to the financial crisis, including some that were backed by loans made by such subprime lenders as New Century, which itself employed three executives who were charged with fraud.

Morgan Stanley also underwrote $37 billion in collateralized debt obligations, the type of deals that lead to a $550 million fine for Goldman. Citigroup and JPMorgan have both also paid fines related to CDOs.

In 2010, Morgan Stanley did agree to pay $102 million to the state of Massachusetts to end a probe relating to Morgan Stanley’s relationship to New Century. No official charges were ever filed. And earlier this year, Morgan Stanley paid $227 million to the Fed. But that was related to foreclosure abuses that took place after the housing bust.

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A case against Morgan Stanley could still materialize. Regulators seem to have recently stepped up their efforts to prosecute financial-crisis-related crimes. U.S. Attorney General Eric Holder says the Justice Department is on the verge of bringing more cases.

But there’s no sign the Justice Department is targeting Morgan Stanley. JPMorgan recently added a disclosure to the legal section of its financial filings saying its mortgage operations are under investigation by the Justice Department. Morgan Stanley says it too has been involved in reviews or investigations by the government. But the wording of those disclosures haven’t changed in three years.

And here’s some more evidence that Morgan Stanley may be in the clear: All banks estimate how much money they could owe in legal fees and fines. JPMorgan says it could owe $6.8 billion. Goldman’s estimate is $3.5 billion. At Bank of America, the number is $2 billion. Morgan Stanley’s estimate: zero, or close to it.

The Justice Department declined to comment. An SEC spokesperson said that it does not comment on cases it hasn’t brought. Morgan Stanley declined to comment as well.

One possible explanation is that Morgan Stanley didn’t do anything wrong in the run up to the financial crisis.

Investors in dozens of deals who have sued the bank seem to disagree. “I have seen no evidence that Morgan Stanley is less culpable than other firms,” says a lawyer who has worked on several cases on behalf of investors who lost money in Morgan Stanley deals. “Having spent the last four-and-a-half years litigating these deals, that’s not what I have found.”

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E-mails and other documents uncovered in a case brought by Washington state’s King County, which lost money on a structured investment that Morgan Stanley helped put together, showed bankers at the firm knew the deal was riskier than they were telling investors. According to one e-mail, a Morgan Stanley banker wrote he was seeing more loans being made to individuals who had bought numerous homes and run up a lot of debt. Other loans looked to have been made on the basis of stated incomes that were not reasonable given the borrowers’ credit scores. “Bottom line,” wrote the banker in an e-mail to colleagues at the bank, “there is not a lot of ‘common sense’ being used when approving these loans.”

Nonetheless, most of those loans, according to King County’s suit, made it into the deal. According to documents filed in the case, one of the loans Morgan Stanley included in the final deal was for $143,000 to buy a vacant lot. An independent broker valued the property at $11,000, according to court documents. Yet Morgan Stanley said the land was worth $183,000.

In April, Morgan Stanley settled the case with King County for an undisclosed amount. It’s a settlement the government might want to take a second look at.