At the end of the movie Bill remarks that the tornado didn't take the house. In fact, it was originally supposed to. The Hardin County, Iowa, Historical Society and many citizens objected to the house being blown up so it was spared. The area is now a tourist attraction as the rubble from the barn and fences is still there exactly as it was in the movie.
During an early scene when Philip Seymour Hoffman is sitting on a lawn chair, he lifts his leg in the air while laughing. His genitals were fully visible for a split second; this was edited out for DVD and VHS releases, but was leaked from VHS screeners sent to industry professionals.
In order to get the background skies looking suitably stormy, the truck cab sequences had to be flooded with high-intensity lighting for contrast. As a result, Helen Hunt and Bill Paxton suffered minor retinal burns through much of the filming.
Trailers contain a shot not in the film: a truck tire hurtling towards the viewer. This was supposedly one of the test shots that was created during pre-production to prove that CGI was capable of executing the effects sequences with the necessary level of realism.
The real town of Wakita, Oklahoma had part of its old downtown area demolished by the film crew for the scenes after the twister passes. The studio then paid for the downtown to be rebuilt. The town also kept the new fire truck used in the film.
The original Director of Photography was Don Burgess (best known for his collaborations with Robert Zemeckis), but he and many other crewmembers walked off the set midway through filming after a series of heated arguments with director Jan de Bont.
The laptops used in the film are Silicon Graphics Indy Presenter LCD screens (not real laptops) that have been modified to look like functional laptops when in fact the screen image is generated by a computer off-screen.
Jan de Bont said he regretted thinking of the hail sequence because it took so long to do and was very difficult. Also the crew couldn't find ice blocks big enough in Oklahoma, so they had to find them in other states.
Many of the news reports spread throughout the movie are actual weathermen from Oklahoma news stations, including Gary England, chief meteorologist at KWTV in Oklahoma City, and Rick Mitchell, chief meteorologist at KOCO in Oklahoma City. The "1969" footage of Gary England giving the televised tornado warning to Jo's family is actual archived footage of him issuing a tornado warning; however, Gary England did not join KWTV until 1972.
An urban legend states that a tornado hit a drive-in theater in the town of Stoney Creek, Ontario while this movie was playing. What really happened was that on May 20, 1996 a tornado hit a drive-in theater in the town of Thorold that was scheduled to play this movie. One of the screens was damaged. The movie was not actually playing when the tornado hit, but scheduled to play that evening.
The base camp (where the crew trucks and equipment was staged) for the end sequence of the film was at a pig farm down the road from the well-house. Every morning the cast and crew were greeted by the aroma of a 2 acre pig-waste holding pond in the middle of all the trucks.
After the team leaves Wakita, there is a seemingly impossible helicopter shot in which the camera descends several hundred feet in a matter of seconds, ending up mere feet from the convoy. This was achieved by having the cars drive slower than usual and then speeding up the film.
Jonas is vilified in the film for selling out to 'corporate sponsors'. This is especially ironic considering the very prominent product placement for Pepsi. When the team is making the 'wings' for the sensors, all the cans are for Pepsi products. Additionally, in almost all the shots showing the 'Doppler', the colors spiral inwards and morph into the Pepsi yin-yang symbol.