- 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! You can ever hear his voice going from words into this deafening roar as his flesh literally decomposes off his bones.
- 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...
- The encounter with Adolf Hitler himself deserves a special mention. Indiana Jones is jostled by the crowd gathered to meet the Fuhrer and by chance, is pushed to meet the man face to face. No words are exchanged, and luckily, Hitler doesn't know what Indiana looks like. Thanks to his disguise, he mistakes Indiana for a fanboy officer and signs the journal, which he thinks is an autograph book, and Indiana Jones escapes meeting with the most powerful and evil man in the world by pure chance. The terror on Indiana's face during the meeting is obvious.
- When Indy and Elsa have to navigate the catacombs and they notice that it is infested with rats; it doesn't help that they are forced to go really close to the rats when navigating the tunnels.
- The Grail Knight's existence. He's been in that tomb for centuries, all alone, with nothing to sustain him but his faith and the waters of the Holy Grail. He doesn't even seem to understand how much time has really passed when Indiana Jones appears and he mistakes him for a knight on a grail quest. Though he does seem to immediately sense Donovan's malevolence when he and Elsa arrive in the chamber, even though he has no idea about the Nazis or knows what the object in Donovan's hand (a pistol) is.
- The look in Elsa's eyes when she picks up the grail and tries to leave with it. Her obsession and the trials she faced to get it has driven her insane.