Less than four minutes into his defence of the 4,000 metres crown on the Paolo Borsellino track, Obree got two red-flag warnings, and was disqualified because officials could not see daylight between his arms and his chest.
His 'downhill skier' posture has never found favour with the governing body, the UCI, and they tried to eliminate it by altering their Rule 49, which includes a definition of a rider's position.
'He has betrayed the spirit of Rule 49,' Jacques Sabathier, the president of the world championship officials, said after a British protest had been thrown out. 'Written laws you can obey,' Sandy Gilchrist, the British manager, said. 'Unwritten ones you cannot, and we are dealing with the unwritten.'
'I knew that they were out to get me. This is like the high jump without the bar,' Obree said. 'No measurement has been defined. It's all pretty vague. Officials told me that there would be two warnings and then disqualification.'
His riding position, which puts him almost flat over his handlebars, and his self-designed and produced bike has also been under fire.
An hour before he began his qualifier Obree was told that 'so long as there is daylight between your arms and your chest you will not be disqualified.' The previous day he and Gilchrist spent an anxious eight hours getting the bike accepted by the UCI officials after a dispute over saddles.
After the new 'toadstool'- shaped saddle, another Obree innovation, was thrown out because it was not 'commercially available', they offered four other saddles. Those too were banned because they had been cut down from conventional saddles, and Obree borrowed the saddle from the mountain bike of a 10-year-old boy, which met the rules as it was available to the public.
It also suited Graeme's style, which he developed because an old shoulder injury prevents him racing on the conventional racing bike with drop handlebars.
The UCI has been fretting about the sport being overtaken by technology, as in Formula One motor racing. They emerged triumphant from a May meeting in Rome having altered Rule 49, which dictates both the rider's position and his equipment.
'We are concerned that the athletic performance is being overshadowed by the technology,' the UCI's president, Hein Verbruggen, has said.
Obree complied with their rules regarding his bike, but yesterday it was the turn of the man. 'I believe that Miguel Indurain is adopting my posture for his attack on my hour record. Will they ban him? I don't think so.'
Chris Boardman was the fastest quarter-finalist, in 4min 25.801sec, beating Spain's Juan Martinez by almost four seconds. Boardman now faces Jens Lehmann of Germany, who he beat to Olympic gold in Barcelona.
Results, Sporting Digest, page 35