2006 U.S. Men's Clay Court Championships – Doubles

Mark Knowles and Daniel Nestor were the defending champions, but lost in the first round this year.

Michael Kohlmann and Alexander Waske won in the final 5–7, 6–4, [10–5], against Julian Knowle and Jürgen Melzer.

Seeds
• # 🇺🇸 Bob Bryan / 🇺🇸 Mike Bryan (quarterfinals)

• # Mark Knowles / 🇨🇦 Daniel Nestor (first round)

• # 🇦🇹 Julian Knowle / 🇦🇹 Jürgen Melzer (final)

• # 🇦🇺 Ashley Fisher / 🇦🇺 Stephen Huss (semifinal)