The Standard & Poor's/Case-Shiller index fell in December from November in all but one of the 20 cities it tracks. The 20-city index declined 1 percent.
The only market to see a gain was Washington, D.C.
Eleven of the markets hit their lowest point since the housing bust, in 2006 and 2007: Atlanta, Charlotte, N.C., Chicago, Detroit, Las Vegas, Miami, New York, Phoenix, Portland, Ore., Seattle and Tampa, Fla.
"Unlike the 2006 to 2009 period when all cities saw prices move together, we see some differing stories around the country, said David M. Blitzer, chairman of the Index Committee at Standard & Poor's.
Some of the worst declines are in cities hit hard by foreclosures, which are forcing prices down. Many people are holding off making purchases because they fear the market hasn't hit bottom yet.
The housing recovery is uneven across the United States, with coastal cities in California and the Northeast faring much better than the Midwest and Southeast. One exception is Dallas, which has avoided some of the big losses seen elsewhere.
The Case-Shiller report measures home price increases and decreases relative to prices in January 2000 and gives an updated three-month average for the metropolitan areas it looks at.