List of Estonian football clubs in UEFA Cup
| Club | Land | Count of part. | M | W | D | L | GF | GA | GD |
|---|---|---|---|---|---|---|---|---|---|
Levadia Tallinn 
(also known as Levadia Tallinn, Levadia Maardu) |
|
5 times
2006-2007, 2004-2005, 2003-2004, 2002-2003, 1999-2000 |
16 | 4 | 2 | 10 | 15 | 26 | -11 |
| Flora Tallinn | |
10 times
2008-2009, 2007-2008, 2006-2007, 2005-2006, 2001-2002, 2000-2001, 1997-1998, 1996-1997, 1995-1996, 1994-1995 |
22 | 2 | 6 | 14 | 10 | 40 | -30 |
| Narva Trans | |
2 times
2007-2008, 2001-2002 |
4 | 1 | 0 | 3 | 3 | 14 | -11 |
| Viljandi Tulevik | |
2 times
2000-2001, 1999-2000 |
4 | 0 | 1 | 3 | 2 | 11 | -9 |
| FC TVMK Tallinn | |
5 times
2008-2009, 2005-2006, 2004-2005, 2003-2004, 2002-2003 |
10 | 0 | 2 | 8 | 6 | 25 | -19 |
| FC Lantana Tallinn | |
2 times
1999-2000, 1996-1997 |
6 | 2 | 1 | 3 | 6 | 14 | -8 |
| Sadam Tallinn | |
1 time
1998-1999 |
2 | 0 | 0 | 2 | 1 | 5 | -4 |
| Summary: | 27 times | 64 | 9 | 12 | 43 | 43 | 135 | -92 | |
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