'''Beware of unmarked spoilers below!'''
* The Conqueror Worm is a gigantic caterpillar-like EldritchAbomination that does nothing except eat, and grow, and eat, and grow some more. If Hellboy and Roger hadn't stopped it, it would have continued doing this until [[ApocalypseHow it has eaten everything on the planet]].
* The Crooked Man's face is extremely [[http://4.bp.blogspot.com/_edfdVc9_vCE/S1R3Eh7Dg8I/AAAAAAAAAog/Ps_JYdvCil8/s400/Hellboy-The+Crooked+Man2.jpg unsettling]].
** From the same story, we get a witch that can take off her skin and turn into a raccoon, the deformed descendants of the colonists who disappeared from Roanoke and the general creepiness of the setting in the Appalachian Mountains.
** The art style is extremely unsettling as well - the witches are nearly as unsettling as the Crooked Man. God help you if you read it at night.
* Hectate's long ascension to become patron Goddess of Witches. To date, her forms include a woman with a snake's lower body, an iron-maiden with glowing blue eyes,a strange robotic hybrid of the first two forms and a desiccated corpse barely clinging on to consciousness (when last we saw her, in her conversation with Grey). She is also the ultimate source of vampirism in the Hellboy-verse
* The Nazi scientist getting sucked into the vortex. His skin gets burned/melted away, reducing him to a skeleton as he screams.
* Kroenen when he's shown without his gasmask and almost completely naked. He's covered with [[CoveredInScars huge, grotesque scars]] from his surgical addiction. His eyelids and upper and lower lips have been completely removed making him look like something that crawled out of the UncannyValley. And it was all self-inflicted.
* The giant tentacled EldritchAbomination coming out of Rasputin's stomach.
* The Tooth Fairies. They sound cute, until you consider the fact that getting caught in a swarm of them means that you are EatenAlive.
* Rasputin getting dragged into the portal. Some of his skin and flesh comes off in little globules, and it looks like his eyes float out of his head. He also is [[FoldSpindleMutilation folded in half]] before entering the portal, getting his pelvis sucked in before the rest of him. Even though he's a Nazi creep, you end up feeling squicked out.
* The destruction of the asylum Liz was in in the first film, by said pyrokinetic's nightmare-guided hand. It exploded while guards and patients were all on site.
** Her childhood victims' fates are also pretty scary, though they're AssholeVictims and deserve what they're getting.
* Rasputin's unnerving ability to turn up ''anywhere'' - the museum where Hellboy first fights Sammael, Liz's room in the mental hospital, even the freaking BPRD.
* The vision Rasputin shows Professor Broom of what the future will be if his plans succeed.