When the Fringe pilot episode was "leaked" onto the internet back in June, J.J. Abrams and crew were quick to point out that the editing was not finished, scenes were missing, and different music would be used. Interestingly, even the "final cut" version we received in the Fringe Press Kit was slightly different from the broadcast. The run times were about the same, so what were the changes?

A lot of very minor edits were scattered throughout, mainly tightening up scenes. For example, some dialogue from an earlier scene between Charlie and Olivia was cut.

The opening title sequence was completely new (you can see the original version here).

Four big changes were added to the story line:

• Olivia tears up seeing John for the first time after the explosion, reinforcing her feelings for him
  
• The entire Steig interrogation scene with Oliva Dunham and Jack Bauer Peter Bishop
• Most of the audio from Steig's tape recorder
• The scene where the dead Agent Scott is wheeled away into the "Leaf" room

Also added was the glyph sequence at the very end, which may be some sort of key to hidden Easter Eggs.

Massive Dynamic not only changed names (from Massic Dynamics), they changed locations. The original building was modeled after the The Royal Ontario Museum, where as the new building is a typical New York skyscraper.

The Synaptic Transfer sequence has subtle changes, mostly a darker mood. The inscription on the Kayak changed from CONSTANT 1.61803 to ZENO, the tombstone changed from BLANK to HE'S NOT DEAD, and the screen monitoring John and Olivia got a makeover (although you can still see the old screen in some shots)

Nina Sharp's robotic are got a slight makeover, making it a little more see-through.