Inspired by the audience response to Dream Theater's heavier songs while on tour, the album was written in three weeks. It was engineered by Doug Oberkircher and mixed by Kevin Shirley. Most of the album was played in concert for the Live at Budokan DVD, however all songs from it have been played live to date.
As mentioned in videos of the recording/writing sessions, which were filmed by Mike Portnoy, (edited by Joey Cruz) the band "cooped themselves in a rehearsal studio" in New York, and wrote the full album from March 10th through April 3rd, in a record time of three weeks, after which they began recording, starting with the drum tracks and ending with the vocals. Also, in the "Chaos In Progress" documentary Portnoy says that they Dream Theater wanted Train of Thought to be a "balls to the wall" album with heavier, darker riffing, exposing them to a number of new metal fans.
Some lyrics of "As I Am" were inspired by Dream Theater's 2003 summer tour with Queensrÿche, described by Mike Portnoy as an "irksome series of shows." According to Portnoy, Queensrÿche guitarist Mike Stone tried giving John Petrucci tips on playing guitar, leading Petrucci to write the lyrics: "Don't tell me what's in, tell me how to write".
"Honor Thy Father" was written about Mike Portnoy's stepfather. When asked about what inspired him to write that song, he stated in an IRC: "I'm not very good at writing love songs, so I decided to write a HATE song!!!"
The lyrics to "Vacant" were inspired by James LaBrie's daughter, who fell into a short coma after suffering a sudden, unexplained seizure three days before her seventh birthday.
"Stream of Consciousness" is the longest Dream Theater instrumental to date (not counting live mash-ups such as "Instrumedley").
Between 5:51 and 6:07 of the song "In the Name of God", there was a hidden composition buried beneath the far louder sounds of the song itself which lay undiscovered for over a year and a half. The band did not tell anyone that a hidden "nugget" (as it became known amongst Dream Theater fans) was present in the song, and only when Mike Portnoy mentioned it in his Mike Portnoy: Live at Budokan Drum-Cam DVD over a year later did someone find it. The Mike Portnoy message board was rife with fans scouring the song looking for what it might be, until a fan going by the pseudonymous name "DarrylRevok" mentioned that from 5:51 to 6:07 there appeared to be morse code audible, which Nick Bogovich (user handle "Bogie") isolated and discovered that when translated to English, the phrase "eat my ass and balls" (a Mike Portnoy catchphrase) was the result.
Jordan Rudess played the final note in the album (heard at 14:06 of "In the Name of God") with his nose as shown in the "Making Train of Thought" documentary. Mike Portnoy approved the take while he was filming. This is also the first note of Octavarium's first song, "The Root of All Evil" and the last note of the last song, "Octavarium" (heard at 23:29).