| Tuesday 19th September 2006 | |||
| Barnsley | 1-2 | Milton Keynes Dons | |
| Birmingham City | 4-1 | Wrexham | aet |
| Brentford | 0-3 | Luton Town | |
| Charlton Athletic | 1-0 | Carlisle United | |
| Crewe Alexandra | 2-0 | Wigan Athletic | |
| Hereford United | 1-3 | Leicester City | |
| Hull City | 0-0 | Hartlepool United | aet |
| (Hull City won on penalties) | |||
| Leeds United | 3-1 | Barnet | |
| Mansfield Town | 1-2 | Portsmouth | |
| Millwall | 0-4 | Southampton | |
| Peterborough United | 1-2 | Everton | |
| Port Vale | 3-2 | Queens Park Rangers | |
| Reading | 3-3 | Darlington | aet |
| (Reading won on penalties) | |||
| Rotherham United | 2-4 | Norwich City | |
| Sheffield United | 1-0 | Bury | |
| Southend United | 3-2 | Brighton and Hove A | |
| Walsall | 1-3 | Bolton Wanderers | |
| Watford | 0-0 | Accrington Stanley | aet |
| (Watford won on penalties) | |||
| West Bromwich Albion | 3-1 | Cheltenham Town | |
| Wednesday 20th September 2006 | |||
| Chesterfield | 2-1 | Manchester City | |
| Doncaster Rovers | 3-3 | Derby County | aet |
| (Doncaster Rovers won on penalties) | |||
| Fulham | 1-2 | Wycombe Wanderers | |
| Middlesbrough | 0-1 | Notts County | |
| Scunthorpe United | 1-2 | Aston Villa | |
