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

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.

[14] Scientists at La Jolla Institute for Immunology study the fundamental workings of the immune 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.