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The story of Dr. John Dorian from his first day as a medical intern, through his residency, to full attending physician. Each episode has Idiosyncratic Episode Naming, almost always "My [something]." Peppered throughout are episodes that switch the narration to another character, named "His Story", "Her Story", or "Their Story".
Season 1
(October 2, 2001 - May 21, 2002)
- "My First Day"
- "My Mentor"
- "My Best Friend's Mistake"
- "My Old Lady"
- "My Two Dads"
- "My Bad"
- "My Super Ego"
- "My Fifteen Minutes"
- "My Day Off"
- "My Nickname"
- "My Own Personal Jesus"
- "My Blind Date"
- "My Balancing Act"
- "My Drug Buddy"
- "My Bed Banter & Beyond"
- "My Heavy Meddle"
- "My Student"
- "My Tuscaloosa Heart"
- "My Old Man"
- "My Way or the Highway"
- "My Sacrificial Clam"
- "My Occurrence"
- "My Hero"
- "My Last Day"
Season 2
(September 26, 2002 - April 17, 2003)
- "My Overkill"
- "My Nightingale"
- "My Case Study"
- "My Big Mouth"
- "My New Coat"
- "My Big Brother"
- "My First Step"
- "My Fruit Cups"
- "My Lucky Day
- "My Monster"
- "My Sex Buddy"
- "My New Old Friend"
- "My Philosphy"
- "My Brother, My Keeper"
- "His Story"
- "My Karma"
- "My Own Private Practice Guy"
- "My T.C.W."
- "My Kingdom"
- "My Interpretation"
- "My Drama Queen"
- "My Dream Job"
Season 3
(October 2, 2003 - May 4, 2004)
- "My Own American Girl"
- "My Journey"
- "My White Whale"
- "My Lucky Night"
- "My Brother, Where Art Thou?"
- "My Advice to You"
- "My Fifteen Seconds"
- "My Friend the Doctor"
- "My Dirty Secret"
- "My Rule of Thumb"
- "My Clean Break"
- "My Catalyst"
- "My Porcelain God"
- "My Screw Up"
- "My Tormented Mentor"
- "My Butterfly"
- "My Moment of Un-Truth"
- "His Story II"
- "My Choosiest Choice of All"
- "My Fault"
- "My Self-Examination"
- "My Best Friend's Wedding"
Season 4
(August 31, 2004 - May 10, 2005)
- "My Old Friend's New Friend"
- "My Office"
- "My New Game"
- "My First Kill"
- "Her Story"
- "My Cake"
- "My Common Enemy"
- "My Last Chance"
- "My Malpractice Decision"
- "My Female Trouble"
- "My Unicorn"
- "My Best Moment"
- "My Ocardial Infarction"
- "My Lucky Charm"
- "My Hypocritical Oath"
- "My Quarantine"
- "My Life in Four Cameras"
- "My Roommates"
- "My Best Laid Plans"
- "My Boss' Free Haircut"
- "My Lips are Sealed"
- "My Big Move"
- "My Faith in Humanity"
- "My Drive-By"
- "My Changing Ways"
Season 5
(January 3, 2006 - May 16, 2006)
- "My Intern's Eyes"
- "My Rite of Passage"
- "My Day at the Races"
- "My Jiggly Ball"
- "My New God"
- "My Missed Perception"
- "My Way Home"
- "My Big Bird"
- "My Half-Acre"
- "Her Story II"
- "My Buddy's Booty"
- "My Cabbage"
- "My Five Stages"
- "My Own Personal Hell"
- "My Extra Mile"
- "My Bright Idea"
- "My Chopped Liver"
- "My New Suit"
- "His Story III"
- "My Lunch"
- "My Fallen Idol"
- "My Déjà Vu, My Déjà Vu"
- "My Urologist"
- "My Transition"
Season 6
(November 30, 2006 - May 17, 2007)
- "My Mirror Image"
- "My Best Friend's Baby's Baby and My Baby's Baby"
- "My Coffee"
- "My House"
- "My Friend with Money"
- "My Musical"
- "His Story IV"
- "My Road to Nowhere"
- "My Perspective"
- "My Therapeutic Month"
- "My Night to Remember"
- "My Fishbowl"
- "My Scrubs"
- "My No Good Reason"
- "My Long Goodbye"
- "My Words of Wisdom"
- "Their Story"
- "My Turf War"
- "My Cold Shower"
- "My Conventional Wisdom"
- "My Rabbit"
- "My Point of No Return"
Season 7
(October 25, 2007 - May 8, 2008)
Season 8
(January 6, 2009 - May 6, 2009)
- "My Jerks"
- "My Last Words"
- "My Saving Grace"
- "My Happy Place"
- "My ABC's"
- "My Cookie Pants"
- "My New Role"
- "My Lawyer's in Love"
- "My Absence"
- "My Comedy Show"
- "My Nah Nah Nah"
- "Their Story II"
- "My Full Moon"
- "My Soul on Fire: Part 1"
- "My Soul on Fire: Part 2"
- "My Cuz"
- "My Chief Concern"
- "My Finale (parts 1 and 2)"
Season 9 (Med School)
(December 1, 2009 - March 17, 2010)