An index that measures changes in the price per square foot of homes for 25 metro areas posted a monthly increase of 3 percent in June, according to real estate data company Radar Logic, with gains in all but two metros.

The 3 percent rise from May to June was one of the largest gains for the month of June in the history of Radar Logic’s price data, which dates back to 2000.

The Boston metro area had the highest monthly gain in price per square foot in June, up 6.5 percent to $200.63, followed by the Atlanta metro area, up 5 percent to $81.19.

An index that measures changes in the price per square foot of homes for 25 metro areas posted a monthly increase of 3 percent in June, according to real estate data company Radar Logic, with gains in all but two metros.

The 3 percent rise from May to June was one of the largest gains for the month of June in the history of Radar Logic’s price data, which dates back to 2000.

The Boston metro area had the highest monthly gain in price per square foot in June, up 6.5 percent to $200.63, followed by the Atlanta metro area, up 5 percent to $81.19.

And the two metros with declines in price per square foot were: Seattle, down 1.6 percent to $182.02, and Milwaukee, down 0.2 percent to $119.66.

Meanwhile, nine of the 25 metros tracked by Radar Logic in its monthly RPX index report experienced year-over-year gains in price per square foot in June. Chicago had a 5.4 percent year-over-year gain in June — the highest among the 25 metros — and Boston was second with a 4.9 percent annual rise.

San Jose and San Francisco shared a 5.7 percent annual decline in June — the largest decline among the 25 metros. Those metros still remain the priciest on the list: the San Jose metro’s price per square foot was $325.72 in June while San Francisco’s was $273.56.

The June index is based on the previous 28 days of RPX values for each market as of June 18, 2009.

All of the metros tracked in the index have seen declines in price per square foot in the past two years, based on two-year annualized data gathered by Radar Logic. Charlotte, N.C., had the slightest two-year decline (-2.8 percent), followed by Columbus, Ohio (-3.1 percent); and Milwaukee (-3.8 percent).

Las Vegas had the largest two-year annualized decline (-31.2 percent), followed by Phoenix (-26.7 percent) and Sacramento, Calif. (-24 percent).

Philadelphia had the highest five-year annualized gain in price per square foot (3.2 percent), followed by Seattle (2.9 percent) and Milwaukee (2.8 percent). Las Vegas had the largest five-year annualized decline (-11.3 percent), followed by Detroit (-9.5 percent) and Sacramento (-8.9 percent).

A separate gauge of transaction counts for the 25 metro areas — which doesn’t necessarily mirror transaction volume for a given market, rose most in Philadelphia, Chicago and San Jose on a year-over-year basis in June, and dropped most in Charlotte, St. Louis and Milwaukee.

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