The magazine's criteria, which focus on surveys and research grants, have been widely criticized for lacking scientific rigor and being little more than a medical beauty contest.
Still, Rubenstein called it "a wonderful endorsement." The real achievement of Penn, now behind only Harvard University, is consistently staying in the top five, he said.
"The fact that we went from three to two, quite frankly, I don't give a lot of weight, but to remain in the top five is outstanding."
After Harvard, Penn, and Johns Hopkins, there was a tie for fourth between the University of California, San Francisco, and Washington University in St. Louis. Duke University, the University of Michigan, the University of Washington, and Yale University tied for sixth. Columbia University rounded out the top 10.
The University of Pittsburgh's medical school, No. 14, was the only other Pennsylvania school in the top 50 this year. The University of Medicine and Dentistry of New Jersey did not make the top 50.
Though the U.S. News rankings are popular among prospective students and admissions officers, many researchers ridicule them.
"Within academic circles, they are dismissed," said William McGaghie, a professor at Northwestern University's Feinberg School of Medicine, which tied for 18th this year.
In a 2001 article for the journal Academic Medicine, McGaghie and a colleague blasted the rankings, saying they "are ill-conceived; are unscientific; are conducted poorly; ignore medical school accreditation; judge medical school quality from a narrow, elitist perspective; and do not consider social and professional outcomes in program quality calculations."
In a phone interview Wednesday, McGaghie said his views had not changed.
"The medical school rankings have no practical value and fail to meet standards of journalistic ethics," the article concluded.
U.S. News used four standards to assess the schools.
The most important was school reputation as assessed through surveys of medical deans, other top academic officers, and directors of residency programs.
Research activity was also key in the rankings. That was measured largely by the amount of grant money each school is awarded by the National Institutes of Health.
Also assessed were the percentage and quality of applicants accepted, based on students' scores on standardized tests and their undergraduate grade point averages, as well as the ratio of full-time faculty to students.
"These metrics are surrogate measures for excellence," Penn's Rubenstein said. "I view them as an indication of overall quality."
Contact staff writer Josh Goldstein at 215-854-4733 or email@example.com.