They won the 2008 Nobel Prize in physics for discoveries that help explain the behavior of the smallest particles of matter.
American Yoichiro Nambu, 87, of the University of Chicago, won half of the 10 million kronor (US$1.4 million) prize for the discovery of a mechanism called spontaneous broken symmetry.
Makoto Kobayashi and Toshihide Maskawa of Japan shared the other half of the prize for discovering the origin of the broken symmetry that predicted the existence of at least three families of quarks in nature.
The academy said the trio "presented theoretical insights that give us a deeper understanding of what happens far inside the tiniest building blocks of matter."
In physics, the idea of symmetry refers a kind of equality or equivalence in a situation. At the subatomic level, for example, you should not be able to tell whether you are watching events unfold directly or in a mirror, or whether a movie of those events is running forward or backward. And particles should behave just like their alter egos, called antiparticles.
If any of these rules is violated, the symmetry is broken.
One big broken symmetry arose immediately after the big bang, when just a tiny bit more matter than antimatter was created. Because these two kinds of particles annihilate each other when they meet, that excess of matter was responsible for seeding the universe.
Nambu introduced his description of spontaneous symmetry violation into particle physics in 1960.
The Nobel citation said Nambu's theories now permeate the Standard Model of physics, which is the basic theory of how the universe operates. For example, they help explain why different particles have different masses.
In 1972, Kobayashi and Maskawa explained why an experiment eight years before had found that some subatomic particles called kaons failed to follow the rules of symmetry. Their explanation predicted the existence of three unknown subatomic particles called quarks. In fact, scientists discovered those predicted particles between 1974 and 1994.
Kobayashi and Maskawa also predicted that symmetry would be broken in the behavior of other particles, called B-mesons. As early as 2001, scientists confirmed that prediction, too.
Nambu said he was awakened by the academy, which called to tell him about the prize.
"I was surprised and honored. I didn't expect it. I've been told for many years that I was on the list (to get the award)," he said. "I had almost given up."
The Japanese-born Nambu moved to the United States in 1952 and is a professor at the Enrico Fermi Institute at the University of Chicago, where he has worked for 40 years. He became a U.S. citizen in 1970.
Kobayashi, 64, works for the High Energy Accelerator Research Organization, or KEK, in Tsukuba, Japan. Maskawa, 68, is a physics professor at Kyoto Sangyo University in Japan's ancient capital of Kyoto, who also teaches at Nagoya University in his hometown in central Japan.
"I wasn't expecting the prize," Kobayashi said. "I've been only pursuing my interest."
"It's an honor to receive the prize for my work from long time ago," Kobayashi said at a news conference in Japan. "I wrote that paper more than 30 years ago."
Kobayashi seemed to be astonished by the big crowd of reporters and said "Looks like it's a big deal."
His news conference was interrupted several times by a phone call from Prime Minster Taro Aso, who congratulated the 64-year-old professor.
In a separate news conference at his university, Maskawa said, "As a scientist, I'm not thrilled by the prize."
"I was happier when our findings were acknowledged around 2002. The Nobel prize is a rather mundane thing."
The last Japanese citizen to win the physics prize was Masatoshi Koshiba of the University of Tokyo in 2002. He shared half of the prize with Raymond Davis Jr. of the U.S. for work in detecting cosmic neutrinos. American Riccardo Giacconi received the other half of the prize for his work that led to the discovery of cosmic X-ray sources.
The 2008 prize is "recognizing one of the most basic and fundamental aspects of existence," said Phil Schewe, a physicist and spokesman for the American Institute of Physics in College Park, Md. "Nature works in strange ways, and these three physicists helped to explain that strangeness in an ingenious way."
On Monday, three European scientists won the Nobel Prize in medicine for separate discoveries of viruses that cause AIDS and cervical cancer.
The prizes in chemistry, literature and the Nobel Peace Prize will be announced later this week, while the economics award will be presented on Monday.