The Hillcrest hospital ranked high in national rankings for geriatrics, nephrology, pulmonology and urology.
The magazine listed Scripps Memorial Hospital second in San Diego and ninth in California. The La Jolla facility scored well nationally in cardiology and heart surgery.
San Diego-area hospitals failed to crack the top 20 nationally in rankings for any of the 16 specialties examined in the study of 5,000 medical facilities around the country.
Scripps Mercy Hospital ranked third in San Diego County, followed by Scripps Memorial Hospital Encinitas, Sharp Memorial Hospital and Grossmont Hospital in La Mesa.
The U.S. News Best Hospitals 2013 guidebook is scheduled to go on sale next month.
"Patients seek out UC San Diego Health System for our ability to provide superior care for the full spectrum of medical needs, including the most serious and rare conditions," said Paul Viviano, CEO of the UC San Diego Health System. "To be recognized for this dedication, at a national level, is a credit to our physicians, nurses and staff."
The magazine and research partner RTI International surveyed nearly 10,000 specialists and went through data on death rates, patient safety and hospital reputation, among other factors.
The top hospitals overall in the U.S. were, in order, Massachusetts General Hospital, Boston; Johns Hopkins Hospital, Baltimore; the Mayo Clinic, Rochester, Minn.; the Cleveland Clinic; and Ronald Reagan UCLA Medical Center in Los Angeles.