Honjo discovered the programmed cell death protein 1 (PD-1). This discovery significantly contributed to the establishment of cancer immunotherapy principle by PD-1 blockade.  Order of authorship in the original publication: Ishida, Agata, Shibahara, Honjo.

In 2018 Honjo shared the Nobel Prize in Physiology or Medicine with James P. Allison “for their discovery of cancer therapy by inhibition of negative immune regulation.”