Boonen won two stages in last year's Tour de France

The 24-year-old broke away from the pack with 10km to go to win the 256km race between Bruges and Meerbeke in six hours 22 minutes and 49 seconds.

German Andreas Klier came home 34 seconds later in second while fellow Belgian Peter van Petegem took third.

Six-time Tour de France winner Lance Armstrong dropped back with 25km to go, finishing three minutes off the lead.

The American is now heading back to the United States to contest the Tour of Georgia.

Boonen engineered his most high-profile victory by choosing not to play to his strengths and wait for a sprint finish, preferring to make his charge for the line early.

"I couldn't wait any longer," Boonen explained.

"I knew I wouldn't be able to win with Eric Zabel and his team-mate (Klier) around. I had to attack."

Italian Alessandro Petachhi, who did not take part in the race, retained his lead at the top the 27-leg ProTour standings.

Petachhi is 12 points ahead of second-placed Oscar Freire, who also did not compete in Belgium because of illness.

Boonen, who won the Grand Prix E3 last week, will aim to continue his run of good form at the Ghent-Wevelgem race on Wednesday.

Tour of Flanders results:

1. Tom Boonen (Belgium / Quick-Step) 6:22:49"
2. Andreas Klier (Germany / T-Mobile) +33"
3. Peter Van Petegem (Belgium / Davitamon - Lotto) +43"
4. Erik Zabel (Germany / T-Mobile)
5. Roberto Petito (Italy / Fassa Bortolo)
6. Alessandro Ballan (Italy / Lampre - Caffita)
7. George Hincapie (US / Discovery Channel) +1:43"
8. Leon van Bon (Netherlands / Davitamon - Lotto)
9. Sergei Ivanov (Russia / T-Mobile)
10. Vladimir Gusev (Russia / Team CSC)
11. Juan Antonio Flecha (Spain / Fassa Bortolo)
12. Karsten Kroon (Netherlands / Rabobank)