The known alternate timelines that existed in the Star Trek universe of stories include:
- The Federation-Klingon battle timeline in "Yesterday's Enterprise" from Star Trek: The Next Generation.
- The past, present, and future timelines that Q has Captain Picard bouncing around in in "All Good Things..." from Star Trek: The Next Generation.
- The timeline created by the Borg in Star Trek: First Contact where they assimilated Earth in the 21st century.
- The Veridian star system destruction timeline in Star Trek: Generations.
- The Year of Hell timeline in "Before And After" from Star Trek: Voyager, where Kes stays on Voyager and marries Tom Paris, having both a daughter and a grandson.
- The Year of Hell timeline in "Year Of Hell" and "Year Of Hell, Part II" from Star Trek: Voyager.
- The timeline in "Timeless" from Star Trek: Voyager where Voyager is knocked out of the quantum slipstream and crash-lands on an icy planet while Chakotay and Kim survive and reach Earth.
- The timeline in "Fury" from Star Trek: Voyager where an elderly Kes kills B'elanna Torres on her way to drain the warp core's energy.
- The various time periods that Voyager was fractured in in "Shattered" from Star Trek: Voyager where an energy surge strikes the ship.
- The timeline in "Endgame" from Star Trek: Voyager where the Voyager crew reaches Earth in 22 years.
- The timeline in the 2009 Star Trek movie where Nero causes Vulcan to implode upon itself by using red matter.
- The timeline where Sisko is "killed" and Deep Space Nine is turned over to the Klingons in Star Trek: DS9 "The Visitor".
- The timeline where Picard was never stabbed and didn't have an artificial heart in Star Trek: TNG "Tapestry".
- The timeline where Enterprise fails to save Earth from the Xindi weapon and Humanity is a few thousand refugees on Ceti Alpha V in Star Trek: ENT "Twilight".
- The timeline where the Nazis have taken the east coast of America in WWII in Star Trek: ENT "Storm Front" and "Storm Front, Part II"
- The timelines seen in Star Trek: TNG "Parallels".
- The timeline the alternate Picard came from in Star Trek: TNG "Time Squared".
- The timelines where the Enterprise-D was destroyed (again and again) in Star Trek: TNG "Cause and Effect".
And at least a few more...