All kick-off times in GMT.
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- Sat, Jan 5, 2013
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| FT | Crewe Alexandra | 1 - 2 | Stevenage |
| FT | Doncaster Rovers | 1 - 0 | Colchester United |
| FT | Scunthorpe United | 0 - 0 | Shrewsbury Town |
| FT | Swindon Town | 4 - 0 | Carlisle United |
| FT | Cowdenbeath | 1 - 1 | Greenock Morton |
| FT | Dumbarton | 0 - 1 | Dunfermline Athletic |
| FT | Hamilton Academical | 1 - 1 | Falkirk |
| FT | Livingston | 2 - 2 | Partick Thistle |
| FT | Raith Rovers | 2 - 0 | Airdrie United |
| FT | Brechin City | 3 - 2 | Alloa Athletic |
| FT | East Fife | 2 - 0 | Albion Rovers |
| FT | Queen of the South | 5 - 1 | Arbroath |
| FT | Stenhousemuir | 2 - 0 | Forfar Athletic |
| FT | Stranraer | 0 - 1 | Ayr United |
| FT | Berwick Rangers | 2 - 0 | East Stirlingshire |
| FT | Clyde | 2 - 3 | Annan Athletic |
| FT | Peterhead | 0 - 1 | Montrose |
| FT | Rangers | 1 - 1 | Elgin City |
| FT | Stirling Albion | 2 - 3 | Queen's Park |
| FT | Levante | 3 - 1 | Athletic Bilbao |
| FT | Granada | 1 - 2 | Valencia |
| FT | Deportivo La Coruña | 1 - 0 | Malaga |
| FT | Sevilla FC | 1 - 0 | Osasuna |
| FT | Racing Santander | 2 - 1 | Ponferradina |
| FT | Recreativo Huelva | 1 - 1 | Sporting Gijon |
| FT | Villarreal | 1 - 3 | Barcelona B |
| FT | AD Alcorcon | 3 - 2 | Real Madrid Castilla |
| FT-Pens | Marseille Consolat | (4)1 - 1(5) | Moulins |
| FT | Belfort | 1 - 3 | Le Havre AC |
| FT | Le Mans | 1 - 2 | Le Poire SV |
| FT-Pens | Savigneux Montbrison | (1)1 - 1(3) | Venissieux Minguettes |
| FT | Amneville | 1 - 2 | Raon-l'Etape |
| FT | Bordeaux Stade | 1 - 0 | Carquefou JA |
| FT | Boulogne | 0 - 1 | Toulouse |
| FT | Chauray FC | 1 - 5 | Lorient |
| FT | Dreux FC | 1 - 5 | AS Nancy Lorraine |
| FT | Montceau | 0 - 1 | Troyes |
| FT-Pens | Rouen | (3)1 - 1(2) | AC Ajaccio |
| FT-Pens | SC Amiens | (3)1 - 1(5) | Evian Thonon Gaillard |
| FT-Pens | St Malo | (2)1 - 1(4) | Vertou |
| FT | Thaon | 0 - 1 | Sochaux |
| FT | Plabennec | 1 - 0 | Stade de Reims |
| FT | Lille | 3 - 2 | Nimes |
| FT | Gil Vicente | 0 - 0 | Guimaraes |
| FT | Rio Ave | 0 - 1 | Olhanense |
| FT | Academica de Coimbra | 4 - 2 | Vitoria Setubal |
| FT | Sporting Lisbon | 0 - 1 | Paços de Ferreira |
| FT | FC Porto | 1 - 0 | CD Nacional de Madeira |
| FT | Asteras Tripoli | 3 - 1 | AEK Athens |
| FT | Platanias | 1 - 1 | Giannina |
| FT | Panathinaikos | 1 - 2 | Levadiakos |
| FT | Dungannon Swifts | 1 - 0 | Lisburn Distillery |
| FT | Glenavon | 2 - 3 | Crusaders |
| FT | Linfield | 5 - 2 | Coleraine |
| FT | Portadown | 1 - 0 | Donegal Celtic |
| FT | Aberystwyth | 4 - 1 | Prestatyn Town |
| FT | Connah's Quay | 1 - 1 | Carmarthen |
| FT | Llanelli | 2 - 2 | Bangor City |
| FT | Port Talbot | 2 - 1 | Bala Town |
| FT | Newtown | 1 - 1 | T.N.S. |