[3][4] It was founded in 1953 by Howard Hughes, an American business magnate, investor, record-setting pilot, engineer,[5] film director, and philanthropist, known during his lifetime as one of the most financially successful individuals in the world.

The institute has an endowment of $22.6 billion, making it the second-wealthiest philanthropic organization in the United States and the second-best-endowed medical research foundation in the world.

The institute was formed with the goal of basic research including trying to understand, in Hughes's words, "the genesis of life itself."

Despite its principles, in the early days it was generally viewed as a tax haven for Hughes's huge personal fortune.

Partly in response to such claims, starting in the late 1950s it began funding 47 investigators doing research at eight different institutions; however, it remained a modest enterprise for several decades.

By 1975, it had also avoided certain stipulations of the 1969 reform act for charitable institutions due to legal filings by Hughes to change its operational status, with his objections going directly to the White House.

[12] In January 1985 the trustees announced they would sell Hughes Aircraft by private sale or public stock offering.

On June 5, 1985 General Motors (GM) was announced as the winner of a secretive five-month, sealed-bid auction.

[18] In 2025, HHMI cancelled their Inclusive Excellence 3 (IE3) program, which was a 6-year (2022-2028) $8.8 million award they had committed to the IMPACT STEM Network, which sought to enhance undergraduate science education and research.