| | episode | air date | countdown | title |
| S05E20 | 2009-01-09 | | Enemy at the Gate | |
| S05E19 | 2009-01-02 | | Vegas | |
| S05E18 | 2008-12-12 | | Identity | |
| S05E17 | 2008-12-05 | | Infection | |
| S05E16 | 2008-11-21 | | Brain Storm | |
| S05E15 | 2008-11-14 | | Remnants | |
| S05E14 | 2008-11-07 | | The Prodigal | |
| S05E13 | 2008-10-24 | | Inquisition | |
| S05E12 | 2008-10-17 | | Outsiders | |
| S05E11 | 2008-10-10 | | The Lost Tribe (2) | |
| S05E10 | 2008-09-26 | | First Contact (1) | |
| S05E09 | 2008-09-19 | | Tracker | |
| S05E08 | 2008-09-12 | | The Queen | |
| S05E07 | 2008-09-05 | | Whispers | |
| S05E06 | 2008-08-22 | | The Shrine | |
| S05E05 | 2008-08-15 | | Ghost in the Machine | |
| S05E04 | 2008-08-01 | | The Daedalus Variations | |
| S05E03 | 2008-07-25 | | Broken Ties | |
| S05E02 | 2008-07-18 | | The Seed | |
| S05E01 | 2008-07-11 | | Search and Rescue (2) | |
| | | | S04E20 | 2008-03-07 | | The Last Man (1) | |
| S04E19 | 2008-02-29 | | The Kindred (2) | |
| S04E18 | 2008-02-22 | | The Kindred (1) | |
| S04E17 | 2008-02-15 | | Midway | |
| S04E16 | 2008-02-08 | | Trio | |
| S04E15 | 2008-02-01 | | Outcast | |
| S04E14 | 2008-01-25 | | Harmony | |
| S04E13 | 2008-01-18 | | Quarantine | |
| S04E12 | 2008-01-11 | | Spoils of War | |
| S04E11 | 2008-01-04 | | Be All My Sins Remember'd (2) | |
| S04E10 | 2007-12-07 | | This Mortal Coil (1) | |
| S04E09 | 2007-11-30 | | Miller's Crossing | |
| S04E08 | 2007-11-16 | | The Seer | |
| S04E07 | 2007-11-09 | | Missing | |
| S04E06 | 2007-11-02 | | Tabula Rasa | |
| S04E05 | 2007-10-26 | | Travelers | |
| S04E04 | 2007-10-19 | | Doppelganger | |
| S04E03 | 2007-10-12 | | Reunion | |
| S04E02 | 2007-10-05 | | Lifeline (3) | |
| S04E01 | 2007-09-28 | | Adrift (2) | |
| | | | S03E20 | 2007-06-22 | | First Strike (1) | |
| S03E19 | 2007-06-15 | | Vengeance | |
| S03E18 | 2007-06-08 | | Submersion | |
| S03E17 | 2007-06-01 | | Sunday | |
| S03E16 | 2007-05-18 | | The Ark | |
| S03E15 | 2007-05-11 | | The Game | |
| S03E14 | 2007-05-04 | | Tao of Rodney | |
| S03E13 | 2007-04-27 | | Irresponsible | |
| S03E12 | 2007-04-20 | | Echoes | |
| S03E11 | 2007-04-13 | | The Return (2) | |
| S03E10 | 2006-09-22 | | The Return (1) | |
| S03E09 | 2006-09-15 | | Phantoms | |
| S03E08 | 2006-09-08 | | McKay and Mrs. Miller | |
| S03E07 | 2006-08-25 | | Common Ground | |
| S03E06 | 2006-08-18 | | The Real World | |
| S03E05 | 2006-08-11 | | Progeny | |
| S03E04 | 2006-08-04 | | Sateda | |
| S03E03 | 2006-07-28 | | Irresistible | |
| S03E02 | 2006-07-21 | | Misbegotten (3) | |
| S03E01 | 2006-07-14 | | No Man's Land (2) | |
| | | S02E20 | 2006-03-10 | | Allies (1) | |
| S02E19 | 2006-03-03 | | Inferno | |
| S02E18 | 2006-02-24 | | Michael | |
| S02E17 | 2006-02-17 | | Coup d'Etat | |
| S02E16 | 2006-02-10 | | The Long Goodbye | |
| S02E15 | 2006-02-03 | | The Tower | |
| S02E14 | 2006-01-27 | | Grace Under Pressure | |
| S02E13 | 2006-01-20 | | Critical Mass | |
| S02E12 | 2006-01-13 | | Epiphany | |
| S02E11 | 2006-01-06 | | The Hive (2) | |
| S02E10 | 2005-09-23 | | The Lost Boys (1) | |
| S02E09 | 2005-09-23 | | Aurora | |
| S02E08 | 2005-09-09 | | Conversion | |
| S02E07 | 2005-08-26 | | Instinct | |
| S02E06 | 2005-08-19 | | Trinity | |
| S02E05 | 2005-08-12 | | Condemned | |
| S02E04 | 2005-08-05 | | Duet | |
| S02E03 | 2005-07-29 | | Runner | |
| S02E02 | 2005-07-22 | | The Intruder | |
| S02E01 | 2005-07-15 | | The Siege (Part 3) | |
| | | S01E20 | 2005-03-25 | | The Siege, Part 2 | |
| S01E19 | 2005-03-18 | | The Siege, Part 1 | |
| S01E18 | 2005-03-11 | | The Gift | |
| S01E17 | 2005-03-04 | | Letters from Pegasus | |
| S01E16 | 2005-02-25 | | The Brotherhood | |
| S01E15 | 2005-02-18 | | Before I Sleep | |
| S01E14 | 2005-02-11 | | Sanctuary | |
| S01E13 | 2005-02-04 | | Hot Zone | |
| S01E12 | 2005-01-28 | | The Defiant One | |
| S01E11 | 2005-01-21 | | The Eye (2) | |
| S01E10 | 2004-09-17 | | The Storm (1) | |
| S01E09 | 2004-09-10 | | Home | |
| S01E08 | 2004-08-27 | | Underground | |
| S01E07 | 2004-08-20 | | Poisoning the Well | |
| S01E06 | 2004-08-13 | | Childhood's End | |
| S01E05 | 2004-08-06 | | Suspicion | |
| S01E04 | 2004-07-30 | | Thirty-Eight Minutes | |
| S01E03 | 2004-07-23 | | Hide and Seek | |
| S01E02 | 2004-07-16 | | Rising, Part 2 | |
| S01E01 | 2004-07-16 | | Rising, Part 1 | |
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