A fundamental process in cell physiology, autophagy is essential for the orderly recycling of damaged cell parts and understanding it better has major implications for health and disease, including cancer.
Ohsumi's discoveries "have led to a new paradigm in the understanding of how the cell recycles its contents," the jury said.
"Mutations in autophagy genes can cause disease, and the autophagic process is involved in several conditions including cancer and neurological disease," the jury added.
It was de Duve who coined the term "autophagy", which comes from the Greek meaning self-eating.
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In what the jury described as a "series of brilliant experiments in the early 1990s", Ohsumi used baker's yeast to identify genes essential for autophagy.
He then went on to explain the underlying mechanisms for autophagy in yeast and showed that similar sophisticated machinery is used in human cells.
When autophagy breaks down, links have been established to Parkinson's disease, type 2 diabetes and other disorders that appear in the elderly.
Intense research is now underway to develop drugs that target autophagy in various diseases.
Ohsumi, 71, received a PhD from the University of Tokyo in 1974. He is currently a professor at the Tokyo Institute of Technology. He is the 23rd Japanese national to win a Nobel prize, and the 6th Japanese medicine laureate.
"This is the highest honour for a researcher," Ohsumi told Japan's public broadcaster NHK.
"My motto is to do what others don't want to do. I thought (cellular breakdown) was very interesting. This is where it all begins. It didn't draw much attention in the past, but we're now in a time when there a bigger focus on it," added Ohsumi.
The medicine prize is awarded by the Nobel Assembly at the Karolinska Institute.