The Ishizakas were co-discoverers in 1966 of the IgE (immunoglobulin E) protein, a molecule that induces allergic reactions in the human body.

[4] In 1991, Kimishige Ishizaka was appointed president and scientific director of the institute and served in the role until his retirement in 1995.

During the next several years, the institute recruited prominent faculty members and formulated a program to accelerate the commercial development of LJI's research and drug discoveries.

[4] That same year, La Jolla Institute of Immunology became the fifth collaborating organization to join the Sanford Consortium for Regenerative Medicine.

[8] In 2013, La Jolla Institute extended its partnership with the Japanese pharmaceutical company Kyowa Hakko Kirin.

[9] In 2015, La Jolla Institute for Immunology announced its affiliation with the UC San Diego Health System.

Scientists at LJI also lead research into genomic sequencing of immune cells and high-resolution imaging of virus/antibody interactions through cryo-electron microscopy.

Scientists at LJI, in collaboration with researchers at the J. Craig Venter Institute, were the first to publish an analysis of potential SARS-CoV-2 epitopes vulnerable to the human immune system.