With 61 stores currently in development and its long-term debt paid off, Austin, Texas-based Whole Foods is poised for growth.

In its most recent earnings call on May 4, the company said its long-term target is 1,000 stores, more than tripling its current 304 stores.Whole Foods targets smaller stores, more locations

“There is plenty of runway left in the United States, and Canada and the United Kingdom hold great promise,” said John Mackey, co-chief executive officer, during the call. “We consider 1,000 stores to be a reasonable indication of our market opportunity as our brand continues to strengthen, consumer demand for natural and organic products continues to increase, and our flexibility on new store size opens up additional market opportunities.”

Rather than the 50,000- and 80,000-square-foot stores the company was opening five to seven years ago, the average size of the 61 new stores in development average just under 40,000 square feet, according to the company’s second-quarter earnings release.

The company plans to open 10 stores in fiscal 2011, 20 in 2012, 22 in 2013 and nine in 2014.

It opened 16 in 2010, averaging 42,600 square feet. So far in 2011, seven stores have opened, averaging 40,000 square feet.

Mackey said the company wants smaller stores in urban settings.

“In places like West Los Angeles, where it’s hard to find big-store real estate, we are opening smaller stores that are more densely located,” he said

The company also is targeting Washington, D.C., San Francisco, Chicago and possibly Manhattan with this kind of development.

New leases were signed in Markham, Ontario, a Toronto suburb; Fullham, England; Tampa, Fla.; Des Moines, Iowa; Chicago; Riverdale, Md.; Wilmington, N.C.; Nashua, N.H.; and Knoxville, Tenn.

The company’s same store sales are up 8.6% year-to-date, Mackey said.