The recording is a type of concept album wherein the five songs which comprise the first disc explore different themes of lifetime struggle, such as alcoholism, loss of faith, self-isolation, sanctity of life and death. The sixth song—a 42-minute track occupying the entire second disc, separated into eight parts—explores the stories of six individuals suffering from various mental illnesses. Particularly represented are bipolar and post-traumatic stress disorder, schizophrenia, post-partum depression, autism and dissociative identity disorder. Furthermore, the title of the album may also allude to the fact that each song on the album could be seen as a different form of inner turbulence, with the six tracks making another reference to the six degrees, along with the apparent reference to the six degrees of separation. The musical styles of each section of the title track are direct reflections of the band's large variety of influences. Classical, folk, jazz and metal styles are present within the track.
"Blind Faith" was written by James LaBrie about questioning religious belief. Also, it is the second longest song LaBrie has written to date, running at 10:21 (the longest is Sacrificed Sons from Octavarium, running at 10:43.) It was also the first time he had written more than one song on an album. The next time would be on Octavarium.
In the song "Misunderstood", John Petrucci wrote and played the guitar solo, and then reversed it. He then learned how to play this reversed version, and after recording it, reversed it once more. This resulted in a solo like the original but with a unique twist to the way the notes sounded. His use of such a technique was predated by George Harrison, on the Beatles song "I'm Only Sleeping".
"The Great Debate" is a non-partisan song dealing with the topic of stem-cell research. It was originally titled "Conflict at Ground Zero" based on the lyrics in the chorus but changed at the last minute to "The Great Debate" due to the 9/11 terrorist attack on New York City (as producers John Petrucci and Mike Portnoy were actually in a Manhattan studio conducting final mixes of the album on the day in question and made the change when all of the news reports started to refer to the site as "Ground Zero.")
The song "Disappear" was written by James LaBrie and was originally titled "Move On". At 6:46, it is the shortest song on the album and it is about death.
The sixth song "Six Degrees of Inner Turbulence", which makes up the entire second CD, is the longest song Dream Theater have recorded to date. The song tells of six people suffering from various syndromes, each of which either is written by Mike Portnoy or John Petrucci. When recording it, they wanted to keep the song at the 20 minutes, but more and more ideas came which resulted in the 42 minute epic. Realising that they would have to cut "Disappear" and "Misunderstood" to keep the album at one CD, their record label was now open for the idea of a double album (Dream Theater had previously been denied on this when recording Falling into Infinity.)
The last chord of "Six Degrees of Inner Turbulence" is the same that opens "As I Am" on the next album Train of Thought.