O'Brien, seven points behind record pace going into the final event, needed a time of 4 minutes, 40.92 seconds or less in the 1,500 meters to get the mark.
But he failed to produce the big effort he needed, finishing last in an official 5 minutes, 10.9 seconds.
"My legs were tired after the first lap," O'Brien said. "I was just plain old tired. I am a sprinter, not a 1,500-meter runner."
O'Brien started with a bang in his record bid Friday, then tapered off.
He opened by winning the 110-meter hurdles in 13.81 seconds, smashing the American decathlon record for the event and matching his best ever in open competition. He then threw the discus 48.10 meters (157 feet, 10 inches), pole vaulted 4.90 meters (16 ft. 3/4 in.) and threw the javelin 62.20 meters.
Those performances, under steamy weather conditions at Petrovsky Stadium, gave O'Brien a total of 8,217 points, with one event remaining.
But the 1,500 meters has always been one of O'Brien's weaker events.
"If the day is like today, I will be tired when I get to the 1,500," O'Brien said Thursday after compiling 4,736 points in the opening five events, putting him 16 ahead of his pace of two years ago. "I'm not a distance runner."
O'Brien's first-day total was the second-best legal score ever, behind the 4,738 he had at Knoxville. O'Brien accumulated 4,747 points in the 1991 U.S. Championships in New York, but the mark was negated because there was no wind gauge for the 100 meters.
With Eduard Hamalainen of Belarus skipping the Goodwill Games to prepare for next month's European Championships at Helsinki, Finland, O'Brien had no one to push him. After the first day, he had a 623-point lead over fellow American Steve Fritz.
"I feel good about Goodwill because I'm not competing against Hamalainen, so there's not an extreme amount of pressure to defend my title or go head-to-head against him," O'Brien said.
"It gives me an opportunity to concentrate on the things I need to do instead of always looking out and saying, 'I've got to beat this guy or that guy to hold onto my No. 1 ranking.'"
After a shaky start Thursday, O'Brien stayed relaxed by listening to music, including Queen's "We Are the Champions" and the rap group Heavy D. and the Boyz.
The tapes, along with unexpectedly strong performances by his competition in the high jump, pumped up O'Brien into a record effort.
He cleared 2.20 meters, matching the American decathlon record set by Jack Hoyt at Santa Barbara, California, in 1991. That brought O'Brien from 145 points off world record pace to 21 back after four events. He then went ahead by winning the 400 meters in 47.73 seconds.
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