Howard Hughes Medical Institute of Bethesda ended a three-month search for a new president yesterday with the appointment of Dr. Purnell Choppin, who for the last two years has served as vice president and chief scientific officer of the institute.

Choppin was chosen from a field of 100 scientists and administrators from around the country.

"The trustees are pleased to be able to appoint as president a distinguished scientist who has already demonstrated great skill at leading the institute into important areas of new science," said Dr. George W. Thorn, chairman of the trustees, in announcing the unanimous selection.

Choppin takes the top post at the institute at a time when the medical research charity is undergoing rapid expansion.

Founded by billionaire Howard Hughes in 1953, the institute for many years had a modest income from its ownership of Hughes Aircraft Corp. But since Hughes Aircraft was auctioned off in 1985 to General Motors Corp., the institute -- with an endowment of $5 billion -- has been transformed into the largest medical charity in the world and a potentially critical player in the biomedical revolution.

The institute's role in supporting biomedical research was dramatically affected by an agreement it reached earlier this year with the Internal Revenue Service, which for years had investigated whether the institute was a device used to shield Hughes Aircraft from taxes.

The institute reached agreement with the IRS in March to pay $35 million to the government and spend at least $100 million more on medical research over the next 10 years than it had planned.

The settlement also allowed the institute to move beyond its traditional practice of funding laboratory units at teaching hospitals around the country and finance direct research grants and scholarships for the first time.

Since 1983, the institute has more than quadrupled its budget to $230 million, with major increases planned for the next few years.

Hughes has also added structural biology as a major new area to its research program, which includes immunology, genetics, neuroscience and cell biology.

"We've got an unprecedented opportunity in private philanthropy, and we intend to make the best of it," said Choppin.

The new president said he sees his major challenge as keeping the institute "lean" despite the generous budget increases and a rapidly growing number of researchers supported by the institute. In the next year alone, research employment is expected to rise from just over 1,000 to 1,600.

Choppin, 58, succeeds Dr. Donald J. Frederickson, who resigned in June after a board of trustees inquiry into his controversial management practices and spending by him and his wife.

Choppin came to the Hughes Institute from The Rockefeller University, where he was the Leon Hess professor of virology. He also was vice president for academic programs and dean of graduate studies.