Kipchoge, 33, is the reigning Olympic champion in the marathon and has run the fastest recorded time over 26.2 miles-a blistering 2 hours and 25 seconds- as part of a Nike-sponsored marketing event past year that wasn't a ratified race.
But Kipchoge produced a stunning performance to take it by a clear 78 seconds.
Kipchoge won Olympic gold in Rio in 2016, plus this year's London Marathon and his run in Berlin now marks him down as one of the greatest marathon runners of all time.
"I lack words to describe this day", Kipchoge said with a smile after the race.
Eliud Kipchoge crosses the line to win the 45th Berlin Marathon and set a new world record in the process. I have trained so well for this race and have full trust in the programs of my coach. "I am team Kenya", said Makueni senator Mutula Kilonzo Junior.
On an extraordinary day of athletics Eliud Kipchoge smashed the world marathon record, moving to within 100 seconds of running the first sub-two hour marathon, before France's Kevin Mayer broke the decathlon world record.
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Kipchoge completed half distance in 61:06, leaving him well on course for the record - even though he raced the final 17km without a pacemaker.
The women's victor was Kenya's Gladys Cherono, who set a women's record for the Berlin race with a time of 2:18:11. I had to focus on the work I had put in in Kenya and that is what helped push me'.
He passed the five kilometre mark in 14:24 and 10km in 29:21. "I was prepared to run my own race early so I wasn't surprised to be alone".
"It was hard running alone, but I was confident". On the roads he has been nearly unstoppable, winning 10 of 11 races over 26.2 miles, including Olympic gold in Rio de Janeiro and three London marathon titles. I also congratulate his compatriots Amos Kipruto & Wilson Kipsang for going out valiantly to bring a 1-2-3 victory for #TeamKenya. Just after the 15K mark, pacers started dropping off. Kipchoge was left with Josphat Boit, who owns a personal best of 59:19 for the half marathon, as his lone rabbit.
As the race progressed, it was now never a question of if, but when he would be breaking the World Record, for the seventh time in the same course, over the last 15 years. The Kenyan first advertised his talents by winning the 2003 world championships over 5,000m as an 18-year-old, and also won Olympic silver and bronze medals on the track before moving to the marathon in 2012.
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