- While travelling to Pankot Palace Willie, obstructed by the odors of the elephant which carries her, pours the integrally of a bottle of perfume on the animal. In film, one finds awhile later the animal which, dissatisfied to be soaked with the kind, stops in the middle of a river and, using his horn, sprinkles its back as well as the momentary one which it transports. This one falls finally into turbid water from the river, which causes general hilarity. In the beginning, the scene was longer. The elephant did not react only to its "freshing up", but also to Willie's vocalizes. Forgetting the hostile jungle, thanks to the perfume, and finding a little of its social context, Willie starts with deployed throat the song heard at the beginning of film. Carried by the melody, Indy and Short Round made in the same way with a song of their vintage. The perfume and the maintaining noise is definitely too much for the elephant which, with a blow of horn, also radically stops the odor and the songs. Indy and Short Round can do nothing else than explode into laughter.
- Right after the first sacrifice Indy makes his way to the center of the Temple to grab the Sankara Stones. Having put the Stones in his pouch he spots a big stone snake on the top of the altar. Originally, Indy was shown touching the stoned snake in awe, but considering his established snake phobia, the filmmakers came up with the idea of Indy adjusting his hat in a hello manner.
- As Indy walks past the Temple's altar, to explore where the mysterious cries he hears are coming from, we see Willie and Short Round's encounter with a group of Thuggee guards. As Shorty is being captured Willie manages to flee back to the catacombs. What has been left out is the part that shows Willie's return to her room.
- In the original cut of the film there was a scene showing a Thuggee guard whipping slave children when he is suddenly struck in the legs by lava exploding from a fissure. Short Round who was digging nearby witnessed the guard's awakening from his possessed state before the Thuggee was dragged away by other guards. This scene explained how Short Round knew what to do to bring Indy out of Kali's "black sleep." Although, of great significance to the plot, this scene was cut from the final film for unknown reasons, most likely to secure a PG rating.
- Many fans have been expressing thoughts regarding Indiana Jones and friends' choice to go back into the mines instead of leaving through Pankot Palace with the rest of the escaped captives. An explanatory scene to this question was shot showing Indy and Willie helping the freed children to cross the lava pit through a makeshift bridge. When the time came for Short Round to cross the pit the bridge had caught fire under the intense heat and Indy and Willie managed to save him in the nick of time from falling in the lava pit. With the bridge crumbled the trio had to find another way out and that was through the mines. As with the above scenes, the most logical explanation for this cut seems to be the pace and not the film's running time, since it ended up at 113 minutes. Even the addition of all of the scenes mentioned on this writing would never push the film over the 120 minute barrier.