Federal regulators overseeing Fannie Mae and Freddie Mac said today they will seek to recoup losses from companies that securitized "private-label" subprime and Alt-A mortgage-backed securities in cases where they discover misrepresentations and breaches of warranty.

The Federal Housing Finance Agency said it has issued 64 subpoenas from unnamed companies to obtain loan documents that would shed light on whether such misrepresentations were made.

FHFA said it’s seeking the contents of loan files, including documents used in the underwriting process such as loan applications and property appraisals. The subpoenas are part of an ongoing inquiry, which may lead to additional subpoenas.

Fannie and Freddie are generally considered to have been minor players in the subprime and Alt-A markets — together, they own or guarantee $5.5 trillion in mortgages, of which about $255 billion are private-label MBS. But those investments have accounted for a disproportionate share of the companies’ losses.

FHFA placed the companies in conservatorship in September 2008, in the wake of rising losses that threatened to jeopardize their ability to guarantee more loans.

Subprime and Alt-A lending was vastly curtailed when the secondary market for private-label MBS collapsed in late 2007. Through Fannie, Feddie, FHA, VA and USDA, the government now buys or guarantees 95 percent of all residential mortgages.

Fannie and Freddie financed or guaranteed more than 70 percent of single-family home purchases in 2009, up from 40 percent in 2006.

Loans guaranteed by the Federal Housing Administration (FHA), Department of Veterans Affairs (VA) and Department of Agriculture (USDA) accounted for another 25 percent of originations in 2009.

The Obama administration has said the government is prepared to stand behind the companies for at least three more years, and has postponed a decision about their fate until Congress passes legislation overhauling regulation of the financial system.

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