Ibitsu is messed up.

Try "mahou shoujo to the end". Still creeps me out...

second Wolf Guy - Ookami no Monshou

"I already decided I'll do it, so even if I die fighting for that cause, that's fine with me."
"Who the hell do you think I am?!"

someone beat me to kami no kodomo it seems but yea thats the only one that i've ever read that made me kinda regret reading it in the first place (it was interesting but oh so fucked up)

only other one i can think of that was bad enough for me to put on here is battle royal which has also been mentioned

Quote from reid1

Tokyo Akazukin It was so twisted and weird... and weird lol.
If we're talking about realistic stories... probably Ciguatera, there is an event that's hard to digest.

Seconded. I still have nightmares 'till this day.

While I don't quite remember any disturbing manga on the top of my head, Ghost Hunt scared the shiet out of me with its' bloody bath arc. I couldn't take a bath for the longest time.

R-18 below
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Detective Horror Series

Tracker BakaBT

this probably isn't what you mean by "disturbing", but there are several shoujos out there that I've read or attempted to read that really disturbed me... the ones where attempted rape or rape was viewed as OK, or where underage sex is OK... stuff like that. The one that immediately comes to mind is Honey Bitter. I just... ugh.

The only one I can think of that was just plain creepy was Cossette no Shouzou.. scared the crap outta me. I'm kinda easy to scare so I don't normally read those sort of things but I thought it was French and not horror and anyway long story short... it creeped me out.

WEBTOONS ヽ( ★ω★)ノ

I... don't know what everyone else considers 'disturbing'.

I've read Kami no Kodomo- interesting, not particularly disturbing.
Haven't started Mahou Shoujo of the End yet. Heard it's pretty good.
Ibitsu was kinda neat, but not that great. Liked the general feel of the story, despite the fact that what I liked about it was what frustrated me most.
Homunculus was excellent- although the same thing that annoyed me about Ibitsu is here too, in that there are no conclusive answers to... anything, really. Talk about frustrating... I can recommend it now, though, since the scanlation is done.

Other stuff I've read that might be 'disturbing' to others: Toukyou Akazukin, Litchi Hikari Club, Corpse Party [whatever manga are translated], Die, Fetish, basically everything by Itou Junji... That's not even getting into the hentai.

I don't think I've actually come across anything that genuinely disturbs me. Well, Silent Hill fills me with a general sense of unease and dawning horror, but that's not a manga.

My boyfriend just said DOLL: IC in a Doll, but that's less disturbing and more... I dunno, depressing? He only read one chapter thus far anyway...

Mai-chan no Nichijou

^By far the most disturbing manga I have ever read and one I wish I could scrub from my mind. Makes Franken Fran look like My Little Ponies. It's truly awful and just thinking about it now is making me uncomfortable.

Quote from Suxinn

I think Battle Royale is the only manga to date that has made me slightly squeamish. There are quite a few other manga that I consider "disturbing," though not in the "ew gore" kind of way but more in the satirical implications (i.e. Franken Fran). Otherwise, I'm not very easily dist ...

Yes... Franken Fran was very, very disturbing... first volume... that poor dude...

berserk
it's the only one I didn't want to continue at times. but well...not because I was shocked but rather disgusted by the developement

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I'm surprised nobody's mentioned Narutaru, but maybe it's because it's not as disturbing as I think it is since it is somewhere in the first fifty manga I've read and therefore left a deeper imprint. I don't know, but it freaked me out. It's not bad, but the somewhat innocent art mixed with such a ... mature (I suppose, is the best word) plot doesn't mesh too well (the characters are young, there's sex, and there's levels of violence that almost reach gore).

I think somebody mentioned 17-Sai.. To date, it's the only manga I've dropped because of how disturbing and wrong it was (although, to be honest, it was also the art).

If you mean disturbing as leaving the reader with an uncomfortable feeling, then these two are the only ones I can remember, but plenty of manga have left me feeling uneasy.

Sorry, this is solely my personal feeling and experience. I never disturbed by manga (that's picture not real, no reason to get disturbed), but once by cartoon named "HAPPY TREE FRIENDS". After I watched that when I kid, I never feel disturbed by any manga or anime. It's different story when you actually go to a war zone or even just see the photo or video from the real thing, that's so disturbing.

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No manga can ever beat My Balls or Domina no Do! as mind disturbing... they are truly fun at times tho.