Tergat's decision comes amid speculation that the reigning New York Marathon title holder is nearing retirement.
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Brazil's Marilson Gomes dos Santos won the men's race in 2:09.58 from Kenya's Stephen Kiogora and Paul Tergat.
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Tergat has also set several world records on the track and the roads.
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The Athens marathon will be Tergat's last for his country, but he will continue to race on as an individual.
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Tergat was scheduled to face the reigning Olympic and world marathon champions Stefano Baldini of Italy and Jaouad Gharib from Morocco.
Kenya's Martin Lel won the men's race in an upset for favourites Haile Gebrselassie and reigning world marathon record holder Paul Tergat.
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Tergat's world record time knocked 43 seconds off the previous best and was the biggest improvement in the world record in five years.
"I will run as long as I am still able to concentrate and to focus, " said Tergat, who has won two Olympic silver medals in the 10, 000m.
Sammy Korir, who finished one second behind Tergat in Berlin to become the second fastest of all time, Chicago Marathon runner-up Daniel Njenga and fellow Kenyan Evans Rutto will also be in action.
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