Dr Yoshinori Ohsumi was awarded the prestigious Nobel Prize for medicine or physiology prize for his work looking into how cells can remain healthy.
Since the 1990s, Yoshinori Ohsumi has been working with baker's yeast to unlock the secret of human cells.
He has been studying a process called autophagy, in which the body's cells destroy and recycle their own components.
Nobel Committee member Maria Massucci says Dr Ohsumi's work helps explain what goes wrong in a range of illnesses, from cancer to Parkinson's disease.
"The discoveries made by Yoshinori Ohsumi have been instrumental in revealing the methods and significance of a fundamental physiological process, and there's growing hope that this knowledge will lead to the development of new strategies for the treatment of many human diseases."
The word autophagy is derived from the Greek words "auto," meaning self, and "phagy," meaning eating
Self-eating cells may not sound like a good thing.
However, the process is an essential natural defence against disease, and failures of autophagy have been linked to the development of age-related diseases such as dementia.
Professor Christer Hoog, of Sweden's Karolinska Institute, explains.
"Your organs and your whole body are constantly being made over again, because you are growing. So you need to get rid of the old stuff, and you need to generate new structures. But in order to get the new structures in place, you have to get rid of the old stuff. So this is very important in physiology. Without it, you cannot grow up."
Scientists have known about autophagy since the 1950s, but Dr Ohsumi's work has helped them discover more about how it works.
The research could lead to the development of drugs for various diseases, including cancer.
Nobel Committee secretary Thomas Perlmann says the Nobel honour caught Mr Ohsumi off-guard.
"He seemed surprised. The first thing he said was, 'Ah.' I think he was actually not maybe expecting this, and he was surprised, but very pleased."
Dr Ohsumi says the prize is a huge honour.
"In recent years, I've unexpectedly received many awards, but the weight of the Nobel prize is on another level."
The winners of the physics, chemistry and peace prizes are to be announced later this week.
