- Donovan's rapid aging after he drinks from the wrong Grail. "He chose poorly", indeed. What's even more terrifying is that he's still attacking Elsa even after he's been reduced to a skeletal corpse, likely realizing she lied to him!
- The entire sequence leading up to that moment was pretty freaky, really. People's heads plopping down the steps at the beginning of the tunnel with no indication of what exactly caused it, the blades that come whipping out of the walls when you can't see anything for the cobwebs, the invisible handspan-wide bridge over the bottomless crevasse...following a film that up until then pretty much tried to be more kid-friendly than the previous two Indy movies, that was some serious Mood Whiplash.
- If you're ophidiophobic, the sequence where Indy gets his famous fear of snakes will likely make your skin crawl.
- Even for a more light hearted film than the previous two, the book burning in Germany and the close encounter with Hitler himself is nothing short of tense.
Henry Sr.: My boy, we're pilgrims in an unholy land...
- During the fight on the ship, one mook falls in the water. Falling in water with no chance of rescue and then drowning or freezing to death is a horrible way to go!