So his form for Uruguay dipped as he found himself starved of first-team chances at Italian giants Juventus.
Victor Pua took over as Uruguay coach halfway through the qualification campaign. His first game in charge was at home to Paraguay.
O'Neill came on in the second half, played badly and was consigned to the international wilderness. Uruguay qualified without him.
As the players danced on the pitch and the fans celebrated on Montevideo's main avenue, few gave much thought to the chances of Fabian O'Neill making the World Cup squad.
But, as 2001 turned to 2002, there were two seperate developments.
First, O'Neill moved on to Perugia. Suddenly he was back in first-team action, playing his way back to form and fitness.
Meanwhile, on the other side of the Atlantic Victor Pua was giving serious thought to Uruguay's World Cup campaign.
One problem kept presenting itself; his team was solid in defence, but in order to stay alive in the competition they would have to score goals and win games.
He began to think about changing the balance of the side - and in the new-model Uruguay there perhaps might be a place for Fabian O'Neill.