The dream sequence with the evil clowns:
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I could have sworn that I spotted Queen Mary in there.
“There are no atheists in foxholes, eh?”-Keith Jennings from the Omen.

Surprised no one said the scene when his bike gets stolen and all you see is the moving clown, broken chains along with that music.
After Pee Wee gets dropped off by Large Marge, the guy retells the story of the fateful night (a night just like tonight and they say it was her ghost. Then it shows a picture of her and you can hear her laugh in the background.
Those 2 scenes used to get me all spooked.
I don't know why the moving clown never scared me the same way Large Marge and the clown doctors did.

Surprised no one said the scene when his bike gets stolen and all you see is the moving clown, broken chains along with that music.
After Pee Wee gets dropped off by Large Marge, the guy retells the story of the fateful night (a night just like tonight and they say it was her ghost. Then it shows a picture of her and you can hear her laugh in the background.
Those 2 scenes used to get me all spooked.

Large Marge scene was scary and that music in the background.

definitely Large Marge.

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"used to" meaning when I was little I would be scared of that scene but not anymore

What the hell do you mean "
used to
?"

Large Marge scene. Enough said.
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the scene where pee wee is going bonkers at Francis it made me not so much scared but uncomfortable. the whole hand knocking at the door sneaking past the butler. The yelling at Francis while he's bathing and locking him and francis in the room. and his ridiculous behavior like only pee wee.
the fortune teller scene madamme ruby freaked me out.Probably because she was conning pee wee about his bike and pee wee was so trusting of her. It's what stirred the pot for the whole adventure but it bothered me.
the nightmare's with the clowns and t-rex were a little scarring now thinking about it.

The Large Marge scene used to scare me when I was little and the clown scene was always a little creepy to me. This is one of the earliest movie memories I have from when I was young, so it's a little vague to me from then, but I still can remember the Large Marge scene specifically being scary to me.

"The entire clown hospital especially the doctor with
the blow torch who pulls down his surgical mask and menacingly laughs
"Naaahhhhhaaaaa!" You do not expect to see a mean expression
painted on his face."
I didn't even know that the doctor was Francis until many years later!

The entire clown hospital especially the doctor with
the blow torch who pulls down his surgical mask and menacingly laughs
"Naaahhhhhaaaaa!" You do not expect to see a mean expression
painted on his face.

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My nephew was petrified of Large Marge. It took days to get him calmed down and for years we were afraid to refer to Large Marge around him for fear of scaring him again. He saw the movie when he was about 4 years old. He is now 15 and even though he won't admit it, I think he's still a little shaky about it.

The giant head in the magic shop and the Large Marge scene. My parents also tell me what when I used to watch Pee-Wee's Playhouse, I was afraid of Jambi the Genie.
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When I was seven, I would run out of the room when Pee Wee knocked down the row of bikers' wheels outside the bar.

The look on the clowns face and the creepy laugh it does when Pee Wee discovers his bike has been stolen !
Pee Wee's dream about the dinosaurs eating his bike
The part where one of the clowns pulls his mask down and does a creepy laugh ,in Pee Wee's other dream,and where it showed Francis dressed as the devil in the same scene.
Large Marge !

The scene with Large Marge scared the living daylights out of me the first time I saw it way back in 1986.
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Yeah the way they focused on that dummy was definitally freaky. And I don't find clowns or dummies frightening in the slightest. But that combo mixed with Burton's absolutely brilliant direction made me skiddish as a kid. Same with the interrogations.

I also used to be scared of the scene where the dinosaur was eating up Pee Wee's bike cause I really thought the scene wasn't a dream

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Alrigth then, but I was still freaky to see that kind of face on a clown.

It's been last summer since Iv'e seen this movie, I now remember the dummy scene, I was never scared of that scene at all but it did make me feel really sad cause Pee Wee has lost his bike.