2006 AIG Japan Open Tennis Championships – Men's singles

Wesley Moodie was the defending champion, but lost in the third round to Roger Federer.

First-seeded Roger Federer won in the final 6–3, 6–3, against Tim Henman.

Seeds
All seeds receive a bye into the second round. • # Roger Federer (champion)

• # 🇪🇸 Tommy Robredo (quarterfinals)

• # Mario Ančić (quarterfinals)

• # 🇬🇧 Andy Murray (second round)

• # 🇫🇮 Jarkko Nieminen (quarterfinals)

• # 🇷🇺 Dmitry Tursunov (third round)

• # 🇺🇸 Robby Ginepri (second round)

• # 🇹🇭 Paradorn Srichaphan (second round)

• # 🇰🇷 Hyung-taik Lee (semifinals)

• # 🇬🇧 Tim Henman (final)

• # 🇩🇪 Björn Phau (second round)

• # 🇦🇷 Juan Mónaco (third round)

• # Wesley Moodie (third round)

• # 🇩🇪 Benjamin Becker (semifinals)

• # 🇺🇸 Vince Spadea (third round)

• # 🇺🇸 Paul Goldstein (second round)