Alternate versions

A German version omits the entire scene where Frank first rapes Dorothy that Jeffrey witnesses from inside her closet, and it is only implied that he raped her.

51 minutes of deleted scenes reappeared in 2011 and were added as a bonus feature on the 2019 Blu-ray released by the Criterion Collection. In 2021, independent filmmaker Felipe M. Guerra re-edited the film, putting all the deleted scenes back in their original place to see how it would look. The result of this experiment, titled "David Lynch's Blue Velvet - Extended Cut", was made available on YouTube. At almost 2h50min, it is the longest and most complete cut of the movie to date - at least until David Lynch himself returned to the material and re-edited the film his way.

Originally running at nearly four hours, Blue Velvet was cut to approximately two hours (120 minutes) for distribution. The missing footage was put in storage and apparently lost for good. Some of the missing scenes are:

• A couple of scenes at the college where Jeffrey attends which takes place during a dance where two of his friends are on the dance floor with him watching when another friend tells him he has a call from home and he learns about his father's stroke and tells his roommate he has to leave immediately.
• The hospital scene is longer with more dialogue with Jeffrey trying to communicate with his incapacitated father in his hospital bed and talking to a doctor who explains his father's condition.
• A scene at Jeffrey's home with the doctor giving Mrs. Beaumont an injection to calm her down over the stress of her husband's plight.
• Jeffrey having coffee with Mrs. Williams as he's waiting to talk to Detective Williams about his find of the severed human ear. Jeffrey also meets Sandy for the first time at the house.
• An extended scene of Jeffrey with Dorothy in her apartment after Frank Booth leaves and finding another severed human ear in the bathroom sink.
• An argument between Jeffrey and Sandy over his continued obsession in the Dorothy Valens case.
• A rooftop scene during Jeffrey's second visit to Dorothy where she confides in him about her messed up life and wants to throw herself off the roof of the building. But Jeffrey stops her and they kiss for the first time.
• A dinner scene where Jeffrey has dinner with Sandy and her parents where her boyfriend Mike joins them and grows suspicious at the table of the relationship between Sandy and Jeffrey.
• A very surreal scene at the seedy nightclub "This Is It" where Frank and his three henchmen take Jeffrey and Dorothy through the dark, dimly lit place filled with topless waitresses, one of them lights her nipples on fire. Frank then beats up a man and throws him across a pool table for not fixing his jacket pockets for he "lost his trophy." This explains how Jeffrey found the missing ear in the field behind the hospital, it apparently fell through a hole in Frank's jacket pocket.
• A final epilogue scene at the police station where Jeffrey and Sandy give their statements to the press of the case and of Williams explaining that they found Dorothy's young son at the nightclub, Frank's henchmen are dead after the shootout at the warehouse, and the nightclub owner Ben and a few others have been apprehended at the club during the raid.