- The Neary family's alternate longer introduction.
- The 5-second flyover of the power company truck.
- The scientists discovery of the freighter in the Gobi desert is included.
- The scene where Roy Neary argues with his wife and locks himself in a shower.
- The Air Force base press conference scene has been restored from the original version.
- The scene where Roy throws dirt, plants and bricks through his kitchen window has been restored from the original version.
- This version does not contain the mothership ending from the "Special Edition", and retains the original 1977 end title music.
- In the O.V. after Barry runs outside his house and into the night, there's a cut to a music box playing "When You Wish Upon a Star" and then to Roy Neary's house, where he receives a phone call from his boss at the power station. In the S.E. after Barry leaves the house we see a panoramic shot of the city at night instead; the next scene shows Roy playing with a toy train in order to explain to his son what a fraction is. There's an argument between Roy, his wife and his kids (they want to go play Goofy Golf, he wants to go see "Pinocchio" but is outvoted). Then Roy's boss calls. The dialogue spoken by Roy's boss is completely different in the S.E.
- After the power outage, the O.V. version shows Roy Neary at the power station where workers are discussing the power failures and his supervisor tells him to go check an area of the city. The Special Edition deletes this scene.
- The S.E. adds a new scene, after Roy see's the UFO flyby on the road: a UFO stops in front of a McDonald's sign and flashes its light on it, as if to read it.
- An old man sees the UFOs fly by on the road and says "They can fly rings around the moon, but we're years ahead of them on the highway". This scene is missing from the S.E.
- The S.E. adds a scene in which U.S. soldiers and scientists discover the ship, the "Cotopaxi" in the Gobi desert. This scene is inserted right after the one where Roy and his wife watch the sky in the spot where he first saw the UFOs.
- A scene where Roy and his wife argue right after he's fired from his job. Roy lies on his bed and looks at a pillow (whose shape resembles the Devil's Tower mountain) The pillow segment was removed in the S.E.
- The S.E. version changes the chronology of sequences from the mid-section of the O.V. In the O.V. the scene where Roy is fired is followed by the scene where he goes back to the road with his camera, which is followed by The India sequence and then Lacombe's auditorium speech. In the S.E. these scenes are flip-flopped. The scene where Roy is fired is followed by the India sequence, which is followed by Lacombe's auditorium speech, followed by the scene where Roy goes back to the road with his camera.
- In the S.E. Lacombe's auditorium speech is slightly longer containing the applause of the dignitaries.
- The S.E. deletes a scene at an Air Force base after Lacombe and the military argue about the best way to scare the population away from the alien's landing area. In the original Jillian is interviewed by reporters about her son's kidnapping, and Roy and Ronnie arrive at the base to attend a press conference about UFOs. Roy draws the shape of the Devil's Tower on a newspaper over the photo of Jillian and the headline "Cosmic Kidnapping". However, the headline is misspelled as 'kidnaping'.
- In the O.V., the dinner/mashed potato sequence begins with the kids arguing at the table. As soon as Roy walks into the room they immediately stop shouting. In the S.E. this portion is deleted and the scene begins with Ronnie handing Toby the mashed potatoes.
- The S.E. adds a sequence where Roy breaks down and he locks himself in the bathroom and goes under the running shower. Ronnie breaks the door open and yells at him, holding him responsible for their family falling apart.
- The scene where Roy tosses bricks and bushes into his house so he can make the Devil's tower replica was almost entirely removed in the S.E. version. The S.E. only includes the portion of the scene where Ronnie actually leaves with the kids.
- When Ronnie leaves Roy and almost runs him over with her car, the O.V. shows him getting back inside the house from a window. This scene is missing from the S.E.
- In the scene where Roy makes his giant model, he briefly stops and glances to see children playing outside. This portion is slightly shortened in the S.E.
- The sequence when Roy arrives in Wyoming and meets Jillian at the train station while the population is being evacuated by the army is shorter in the S.E.: in the original we saw Roy trying to convince a soldier (played by Carl Weathers) to let him go look for his "sister": the guard says he has orders to shoot anyone that trespasses.
- The S.E. adds a new ending that shows what happens after Roy enters the mothership, with light/sound special effects by Douglas Trumbull.
- In the S.E. the end title music is different. Instead of the closing "overture" music originally commissioned for the credits, we hear an arrangement of "When You Wish Upon A Star".
