| Tourney Name: | Commonwealth of Independent States Cup |
| Year: | 2006 |
| Other Titles: | CIS Cup, Кубок Содружества 2006 |
| Country: | Russia |
| Dates: | 14–22 January 2006 |
| Num Teams: | 16 |
| Venues: | 2 |
| Cities: | 1 |
| Champion Other: |  Neftchi Baku |
| Count: | 1 |
| Matches: | 30 |
| Goals: | 84 |
| Top Scorer: |  Yevhen Seleznyov(5 goals) |
| Prevseason: | 2005 |
| Nextseason: | 2007 |
The 2006 Commonwealth of Independent States Cup was the fourteenth edition of the competition between the champions of former republics of Soviet Union. It was won by Neftchi Baku for the first time.
| Team | Qualification | Participation | |
|---|---|---|---|
 CSKA Moscow | 2005 Russian Premier League champions 1 | 2nd | |
| Shakhtar Donetsk | 2004–05 Vyshcha Liha champions 2 | 3rd | |
 Shakhtyor Soligorsk | 2005 Belarusian Premier League champions | 1st | |
| FBK Kaunas | 2005 A Lyga runners-up 3 | 8th | |
 Liepājas Metalurgs | 2005 Latvian Higher League champions | 1st | |
 TVMK Tallinn | 2005 Meistriliiga champions | 1st | |
 Sheriff Tiraspol | 2004–05 Moldovan National Division champions | 5th | |
 Dinamo Tbilisi | 2004–05 Umaglesi Liga champions | 10th | |
 Pyunik Yerevan | 2005 Armenian Premier League champions | 7th | |
| Neftchi Baku | 2004–05 Azerbaijan Top League champions | 5th | |
 Aktobe | 2005 Kazakhstan Premier League champions | 1st | |
 Pakhtakor Tashkent | 2005 Uzbek League champions | 5th | |
 Vakhsh Qurghonteppa | 2005 Tajik League champions | 2nd | |
 HTTU Ashgabat | 2005 Ýokary Liga champions | 1st | |
 Dordoi-Dynamo Naryn | 2005 Kyrgyzstan League champions | 2nd | |
| Russia U19 | Unofficial entry, not eligible to advance past group stage | 7th |
----
----
----
----
----
----
----
----
1 Neftchi were awarded a win after Pyunik refused to play against Azerbaijani club for safety concerns (related to ongoing Nagorno-Karabakh conflict).[1]
| Rank | Player | Team | Goals | |
|---|---|---|---|---|
| 1 | Yevhen Seleznyov | Shakhtar Donetsk | 5 | |
| 2 | Zayniddin Tadjiyev | Pakhtakor Tashkent | 4 | |
| align=center rowspan="5" | 3 | Branimir Subašić | Neftchi Baku | 3 |
| Aleksandr Salugin | CSKA Moscow | 3 | ||
| George Florescu | Sheriff Tiraspol | 3 | ||
| Aliaksei Kuchuk | Sheriff Tiraspol | 3 | ||
| Ģirts Karlsons | Liepājas Metalurgs | 3 |