Second Round
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Southern-Mediterranean region | ||||
| MFC Sopron | 3–4 | Kayserispor | 3–3 | 0–1 |
| Farul Constanţa | 3–2 | PFC Lokomotiv Plovdiv | 2–1 | 1–1 |
| FK Zeta1 | 1–4 | NK Maribor | 1–22 | 0–2 |
| Maccabi Petah Tikva FC | 4–2 | NK Zrinjski | 1–13 | 3–1 |
| NK Osijek | 2–2(a) | Ethnikos Achna FC | 2–2 | 0–0 |
| Central-East region | ||||
| Grasshopper-Club Zürich | 4–0 | FK Teplice | 2–0 | 2–0 |
| FC Nitra | 2–3 | FC Dnipro Dnipropetrovsk | 2–1 | 0–2 |
| SV Ried | 4–1 | FC Dinamo Tbilisi | 3–1 | 1–0 |
| FC Tiraspol | 4–1 | Lech Poznań | 1–0 | 3–1 |
| FC Moskva | 3–0 | MTZ-RIPO Minsk | 2–0 | 1–0 |
| Northern region | ||||
| Tampere United | 3–5 | Kalmar FF | 1–2 | 2–3 |
| Odense BK | 3–1 | Shelbourne F.C. | 3–0 | 0–1 |
| Lillestrøm S.K. | 6–3 | Keflavik ÍF | 4–1 | 2–2 |
| Hibernian F.C. | 8–0 | Dinaburg FC | 5–0 | 3–0 |
1FK Zeta qualified for this season's UEFA competitions as member of the Football Association of Serbia and Montenegro during the 2005/06 season but was at the time of this match already a member of the Football Association of Montenegro.
2played at FK Partizan's ground in Belgrade, Serbia, because FK Zeta's ground in Golubovci doesn't meet UEFA standards
3played in Herzliya because Maccabi Petah Tikva's ground in Petah Tikva is undergoing renovations
Read more about this topic: 2006 UEFA Intertoto Cup
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