The U.S. Commerce Department reports that new home sales fell 11.2% in January, to 309,000 units on a seasonally adjusted basis. That’s the lowest number in almost 50 years. Experts had expected an increase of 5%.

Yesterday, First American CoreLogic reported that nearly one-fourth of all U.S. residential mortgages are underwater at the end of the fourth quarter of 2009.

That’s more than double the 10.7% rate at the end of the 2009 third quarter. All together, negative equity and near-negative equity (less than 5% equity) totaled almost 29% of all U.S. mortgages.

The FDIC’s Quarterly Banking Report lists 702 problem banks at the end of 2009, compared with 252 at the end of 2008. The number of bank failures in 2009 totaled 140, up from 25 in 2008 and 3 in 2007. So far in 2010, 20 banks have failed.

It should be no surprise that the largest banks (more than $10 billion in assets) reported the only positive return on assets of any sector in the FDIC report. Aside from the usual suspects, this group includes regional banks like PNC Financial Services Group (PNC), Regions Financial Corp. (RF), Fifth Third Bancorp (FITB) and SunTrust Banks, Inc. (STI).

Of the four banks named here, only PNC and Fifth Third showed positive return on assets in the fourth quarter of 2009. And in both cases, the return was less than 1%.

And don’t even ask about the homebuilders. Without federal tax credits, neither Beazer Homes USA Inc. (BZH) or KB Homes (KBH) would have shown a profit in the December quarter. Other homebuilders were in the same boat.

It’s true that homebuilders as a group are crushing the S&P 500 so far this year, up more than 13% compared with a loss of more than 3% on the S&P 500. But that’s based on the hope of an economic recovery leading to increased lending and more building.

And hope is not a plan. As long as unemployment stays high, small and mid-sized banks are in real danger of non-payment of mortgages. And homebuilders relying on federal tax breaks won’t get that support indefinitely.

Just looking at today’s news should give an investor pause before committing to either the homebuilders or the small and mid-sized banks. With a quarter of U.S. residential mortgages underwater more foreclosures are a certainty, which will hurt the banks’ earnings and put more homes on the market, hurting the builders.

The only good news about the outlook for mortgages and homebuilders is that the news could be worse.

Tell us what you think here.

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