The 1999–2000 Heineken Cup was the fifth edition of the Heineken Cup of rugby. Teams from France, Ireland, Italy, Wales, England and Scotland were divided into six pools of four and played home and away matches against each other. The pool winners and two best runners-up qualified for the knockout stages.
Teams
{| class="wikitable" width=100%
|-
! France
! England
! Wales
! Scotland
! Ireland
! Italy
|- valign=top
|
- Stade Français
- Toulouse
- Bourgoin
- Colomiers
- Montferrand
- Grenoble
|
- Leicester Tigers
- Bath
- London Wasps
- Saracens
- Harlequins
- Northampton Saints
|
- Swansea
- Llanelli
- Pontypridd
- Cardiff
- Neath
|
- Glasgow Caledonians
- Edinburgh Reivers
|
- Leinster
- Munster
- Ulster
|
- Petrarca
- Benetton Treviso
|}
Pool stage
In the pool matches teams received
- 2 points for a win
- 1 points for a draw
Pool 1
{| class="wikitable" style="text-align:center"
|-
!width="200"|Team
!width="20"|P
!width="20"|W
!width="20"|D
!width="20"|L
!width="20"|Tries for
!width="20"|Tries against
!width="30"|Try diff
!width="20"|Points for
!width="20"|Points against
!width="25"|Points diff
!width="20"|Pts
|- bgcolor="#ccffcc"
|align="left"| Stade Français
|6||4||0||2||22||9||13||192||109||83||8
|-
|align="left"| Leinster
|6||4||0||2||12||17||−5||150||138||12||8
|-
|align="left"| Glasgow Caledonians
|6||2||0||4||14||23||−9||130||179||−49||4
|-
|align="left"| Leicester Tigers
|6||2||0||4||12||11||1||127||173||−46||4
|}
Pool 2
{| class="wikitable" style="text-align:center"
|-
!width="200"|Team
!width="20"|P
!width="20"|W
!width="20"|D
!width="20"|L
!width="20"|Tries for
!width="20"|Tries against
!width="30"|Try diff
!width="20"|Points for
!width="20"|Points against
!width="25"|Points diff
!width="20"|Pts
|- bgcolor="#ccffcc"
|align="left"| Toulouse
|6||5||0||1||24||5||19||200||73||127||10
|-
|align="left"| Bath
|6||4||0||2||15||8||7||170||80||90||8
|-
|align="left"| Swansea
|6||3||0||3||14||13||1||126||137||−11||6
|-
|align="left"| Petrarca
|6||0||0||6||11||38||−27||76||282||−206||0
|}
Pool 3
{| class="wikitable" style="text-align:center"
|-
!width="200"|Team
!width="20"|P
!width="20"|W
!width="20"|D
!width="20"|L
!width="20"|Tries for
!width="20"|Tries against
!width="30"|Try diff
!width="20"|Points for
!width="20"|Points against
!width="25"|Points diff
!width="20"|Pts
|- bgcolor="#ccffcc"
|align="left"| Llanelli
|6||5||0||1||17||8||9||152||86||66||10
|- bgcolor="#ccffcc"
|align="left"| London Wasps
|6||5||0||1||16||9||7||163||99||64||10
|-
|align="left"| Bourgoin
|6||2||0||4||14||14||0||140||162||−22||4
|-
|align="left"| Ulster
|6||0||0||6||4||20||−16||71||179||−108||0
|}
Pool 4
{| class="wikitable" style="text-align:center"
|-
!width="200"|Team
!width="20"|P
!width="20"|W
!width="20"|D
!width="20"|L
!width="20"|Tries for
!width="20"|Tries against
!width="30"|Try diff
!width="20"|Points for
!width="20"|Points against
!width="25"|Points diff
!width="20"|Pts
|- bgcolor="#ccffcc"
|align="left"| Munster
|6||5||0||1||19||14||5||188||132||56||10
|-
|align="left"| Saracens
|6||3||0||3||24||15||9||206||153||53||6
|-
|align="left"| Colomiers
|6||2||0||4||13||20||−7||144||194||−50||4
|-
|align="left"| Pontypridd
|6||2||0||4||13||20||−7||106||165||−59||4
|}
Pool 5
{| class="wikitable" style="text-align:center"
|-
!width="200"|Team
!width="20"|P
!width="20"|W
!width="20"|D
!width="20"|L
!width="20"|Tries for
!width="20"|Tries against
!width="30"|Try diff
!width="20"|Points for
!width="20"|Points against
!width="25"|Points diff
!width="20"|Pts
|- bgcolor="#ccffcc"
|align="left"| Cardiff
|6||4||1||1||14||13||1||168||141||27||9
|- bgcolor="#ccffcc"
|align="left"| Montferrand
|6||4||0||2||19||6||13||154||85||69||8
|-
|align="left"| Benetton Treviso
|6||2||0||4||6||16||−10||100||167||−67||4
|-
|align="left"| Harlequins
|6||1||1||4||8||12||−4||120||149||−29||3
|}
Pool 6
{| class="wikitable" style="text-align:center"
|-
!width="200"|Team
!width="20"|P
!width="20"|W
!width="20"|D
!width="20"|L
!width="20"|Tries for
!width="20"|Tries against
!width="30"|Try diff
!width="20"|Points for
!width="20"|Points against
!width="25"|Points diff
!width="20"|Pts
|- bgcolor="#ccffcc"
|align="left"| Northampton Saints
|6||5||0||1||19||7||12||184||87||97||10
|-
|align="left"| Grenoble
|6||3||0||3||13||15||−2||110||140||−30||6
|-
|align="left"| Edinburgh Reivers
|6||3||0||3||13||19||−6||112||158||−46||6
|-
|align="left"| Neath
|6||1||0||5||13||17||−4||128||149||−21||2
|}
Seeding
{| class="wikitable" style="text-align:center"
|-
!Seed
!Pool winners
!Pts
!TF
!+/−
|-
|1
|align=left| Toulouse
|10||24||+127
|-
|2
|align=left| Northampton Saints
|10||19||+97
|-
|3
|align=left| Munster
|10||19||+56
|-
|4
|align=left| Llanelli
|10||17||+66
|-
|5
|align=left| Cardiff
|9||14||+27
|-
|6
|align=left| Stade Français
|8||22||+83
|-
!Seed
!Pool runners-up
!Pts
!TF
!+/−
|-
|7
|align=left| London Wasps
|10||16||+64
|-
|8
|align=left| Montferrand
|8||19||+69
|-
| —
|align=left| Bath
|8||15||+90
|-
| —
|align=left| Leinster
|8||12||+12
|-
| —
|align=left| Saracens
|6||24||+53
|-
| —
|align=left| Grenoble
|6||13||−30
|}
Knockout stage
Quarter-finals
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Semi-finals
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