Andre Agassi defeated Todd Martin in the final, 6–4, 6–7(5–7), 6–7(2–7), 6–3, 6–2 to win the men's singles tennis title at the 1999 US Open. It was his second US Open title and fifth major title overall. With the win, Agassi returned to the world No. 1 singles ranking, ultimately ending Pete Sampras' record streak of six year-end No. 1 rankings. Pat Rafter was the two-time defending champion, but lost to Cédric Pioline in the first round after succumbing to shoulder tendinitis.

Seeds

• 🇺🇸 Pete Sampras (withdrew due to back injury) • 🇺🇸 Andre Agassi (champion) • 🇷🇺 Yevgeny Kafelnikov (semifinals) • 🇦🇺 Pat Rafter (first round, retired due to shoulder injury) • 🇧🇷 Gustavo Kuerten (quarterfinals) • 🇬🇧 Tim Henman (first round) • 🇺🇸 Todd Martin (final) • 🇪🇸 Carlos Moyá (second round) • 🇬🇧 Greg Rusedski (fourth round) • 🇨🇱 Marcelo Ríos (fourth round) • 🇦🇺 Mark Philippoussis (withdrew due to left knee injury) • 🇳🇱 Richard Krajicek (quarterfinals) • 🇪🇸 Àlex Corretja (first round) • 🇩🇪 Tommy Haas (fourth round) • 🇩🇪 Nicolas Kiefer (third round) • 🇪🇨 Nicolás Lapentti (second round) • 🇪🇸 Félix Mantilla (first round)

Qualifying draw

Draw

Finals

Top half

Section 1

Section 2

Section 3

Section 4

Bottom half

Section 5

Section 6

Section 7

Section 8