In an analysis of housing affordability, RealtyTrac found that the estimated monthly house payment for a median-priced, three-bedroom home purchased at the end of 2013 was a whopping 21 percent higher than it was at the end of 2012 in more than 300 U.S. counties. That includes mortgage, insurance, taxes, maintenance and the subtracted income tax benefit.
(Read more: Spring thaw may not heat up this housing market)
The rise is the result of higher home prices and higher mortgage rates. RealtyTrac used a 30-year fixed-rate mortgage with an interest rate of 4.46 percent and a 20 percent down payment. That is versus a 3.35 percent interest rate the previous year.
Some metro regions, especially in California and parts of Michigan, saw monthly house payments rise about 50 percent from a year ago.
(Read more: Home builder sentiment index logs sharpest drop ever)
"Home prices were boosted by cash buyers in 2013, and as the cash buyers move out of the market in 2014, the buyers left are not going to be able to afford the home prices as readily in some of these markets," added Blomquist.
It will now take far higher incomes in these markets for potential buyers to afford a purchase. In Los Angeles County, for example, the minimum qualifying income needed to buy a median-priced home is now more than $95,000, compared with about $68,000 a year ago, according to RealtyTrac. Income growth in the U.S. has not been robust to say the least in these last few years.
While it is still cheaper to own than to rent in the vast majority of U.S. housing markets, the scales have tipped the other way in some major metros, like Seattle, Los Angeles, San Francisco, Chicago, Denver and Suffolk County, N.Y. (the Hamptons). The 29 counties where RealtyTrac found it more expensive to own than rent account for 20 percent of the population of the 325 counties it analyzed.