This article details the 2006–07 UEFA Cup qualifying rounds. Times are CEST (UTC+2), as listed by UEFA (local times, if different, are in parentheses).

Round and draw dates

All draws held at UEFA headquarters in Nyon, Switzerland. Matches may also be played on Tuesdays or Wednesdays instead of the regular Thursdays due to scheduling conflicts.

Teams

Below are the 100 teams involved in the qualifying rounds, grouped by their starting rounds. The 32 winners of the second qualifying round qualified for the first round.

First qualifying round

Seeding

Summary

<section begin=Q1 /> These matches were held on 13 July and 27 July 2006. !colspan="5"|Southern-Mediterranean region !colspan="5"|Central-East region !colspan="5"|Northern region

Matches

Tirana won 3–1 on aggregate. CSKA Sofia won 5–1 on aggregate. Litex Lovech won 6–0 on aggregate. Sarajevo won 5–0 on aggregate. Domžale won 7–0 on aggregate. Dinamo București won 9–1 on aggregate. APOEL won 7–1 on aggregate. Omonia won 4–3 on aggregate. Lokomotiv Sofia won 3–1 on aggregate. Roeselare won 7–2 on aggregate. Rapid București won 6–0 on aggregate. Vaduz won 4–1 on aggregate. Zimbru Chișinău won 3–2 on aggregate. Young Boys won 4–1 on aggregate. 2–2 on aggregate; Fehérvár won on away goals. 1–1 on aggregate; Dinamo Minsk won on away goals. Karvan won 2–0 on aggregate. 2–2 on aggregate; Ameri won on away goals. BATE Borisov won 3–0 on aggregate. Basel won 3–1 on aggregate. Artmedia won 3–2 on aggregate. Drogheda United won 4–2 on aggregate. Brøndby won 3–1 on aggregate. Llanelli won 2–1 on aggregate. Skonto won 5–0 on aggregate. Åtvidaberg won 7–0 on aggregate. Ventspils won 4–1 on aggregate. Brann won 2–0 on aggregate. 2–2 on aggregate; Randers won on away goals. Kaunas won 4–1 on aggregate. Sūduva won 2–1 on aggregate. Levadia Tallinn won 2–1 on aggregate. Start won 4–0 on aggregate. 1–1 on aggregate; Flora Tallinn won on away goals. Derry City won 2–0 on aggregate.

Second qualifying round

Seeding

Summary

<section begin=Q2 /> These matches were held on 8 and 10 August (first leg) and 24 August (second leg) 2006. !colspan="5"|Southern-Mediterranean region !colspan="5"|Central-East region !colspan="5"|Northern region 1Due to the [armed conflict going on in Israel](https://bliptext.com/articles/2006-israel-lebanon-conflict), UEFA decided that no European matches could be staged in the country until further notice. Hapoel Tel Aviv's home match was moved to [Tilburg](https://bliptext.com/articles/tilburg), Netherlands, Beitar Jerusalem's to [Sofia](https://bliptext.com/articles/sofia), [Bulgaria](https://bliptext.com/articles/bulgaria) and Bnei Yehuda Tel Aviv's to [Senec, Slovakia](https://bliptext.com/articles/senec-slovakia)<section end=Q2 />

Matches

Trabzonspor won 2–1 on aggregate. Hapoel Tel Aviv won 4–2 on aggregate. 1–1 on aggregate; CSKA Sofia won on away goals. Ethnikos Achna won 6–2 on aggregate. Auxerre won 5–2 on aggregate. Dinamo București won 2–1 on aggregate. Partizan won 3–2 on aggregate. Rapid București won 2–1 on aggregate. Lokomotiv Sofia won 6–0 on aggregate. Litex Lovech won 2–1 on aggregate. Kayserispor won 5–1 on aggregate. Artmedia won 5–3 on aggregate. Sion won 1–0 on aggregate. Grasshopper won 3–1 on aggregate. Slavia Prague won 2–0 on aggregate. 1–1 on aggregate; Chornomorets Odesa won on away goals. 2–2 on aggregate; Basel won on away goals. Metalurh Zaporizhya won 3–0 on aggregate. Wisła Kraków won 2–1 on aggregate. Hertha BSC won 3–2 on aggregate. Rubin Kazan won 5–0 on aggregate. 3–3 on aggregate; Marseille won on away goals. 1–1 on aggregate; Start won 11–10 on penalties Odense won 6–1 on aggregate. Randers won 3–2 on aggregate. Levadia Tallinn won 2–1 on aggregate. Newcastle United won 1–0 on aggregate. 4–4 on aggregate; Åtvidaberg won on away goals. Molde won 2–1 on aggregate. Brøndby won 4–0 on aggregate. Club Brugge won 7–2 on aggregate. Derry City won 7–3 on aggregate.