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- Dragons in The Vision of Escaflowne have a magical gemstone at their heart that can then be used to power guymelefs.
- Organ replacement version in Busou Renkin: Kazuki has a Kakugane in his chest because he blundered into a monster and died, kicking off the plot.
- In GaoGaiGar, Gai Shishioh's cybernetic body is powered by a G-Stone.
- The Super Hero Darkhawk is a humanoid example, bearing a ruby amulet inside of his chest. At one point, the villain Tombstone tore it out, believing it was valuable. Darkhawk recovered
- Requiem Vampire Knight: Dragons are killed for the large gemstone that forms naturally in their body.
- The MacGuffin in XXXenophile: Heart of Stone was a massive ruby carved from the heart of a monster that induced lust in anyone who touched it with their bare flesh.
- Superman's enemy Metallo is called "The Man With The Kryptonite Heart!" since his robotic body is powered by a chunk of kryptonite.
- In Sucker Punch, when Babydoll kills the baby dragon, it has rubies in its throat that she strikes together to spark a fire.
- Ancient men believed in a stone called a Draconite, which had to be removed from a dragon while it still lived (sites of origin being rumored to include the brain and the heart, this was no simple task). True to the trope, draconites were believed to have magical powers.
- In Juliet E McKenna's Aldabreshin Compass series, natural dragons have a gem that relates to their element for a heart. Unnatural dragons created by wizards will fight very hard against natural dragons because the unnatural seeks to replace the void in its heart with the gem from its natural cousin (and occasionally they will break free of the wizard's control if they can feed on enough gemstones; this is why it is vitally important not to summon a dragon near your treasury). It goes without saying, then, that summoning a dragon is reserved for when things have crossed the Godzilla Threshold.
- Greatshells such as the Chasmfiends in The Stormlight Archive by Brandon Sanderson have gems like raw rubies, emeralds, and sapphires deep beneath their shells. By the time of the story, most of these Gem Hearts are gathered through the slightly unsporting method of waiting until the greatshell is pupating, then cutting through the stone carapace to get to the gem.
- Dragons in Eragon have a gemlike organ called an Eldunari. In a twist, though, it has no intrinsic value; it's actually the dragon's emergency Soul Jar.
- Two in Michael Moorcock's works:
- In Cornelia Funke's Dragon Rider, Nettlebrand has a golden casket that acts as his heart. It has no actual value, though.
- Discworld trolls have diamond teeth in order to chew through the stone and gems they eat.
- Played with in The Hero and the Crown, where the last drop of blood a dragon spills before dying turns into a bloodstone (read: ruby).
- The Heroes of Olympus has Alcyoneus who has a body made entirely of jewels and precious metals.
- In the In Her Name series, a genoth is a dinosaur-type alien that has gem eyebrows. They have to be removed very soon after the creature is killed for them to be gems, otherwise they quickly fade and crack, becoming worthless.
- In Everworld, our heroes actually get this in one book—after being drafted by the dragon Nidhoggr to recover some stolen items, he magically replaces the hearts of David, April, Jalil and Christopher with rubies which will kill them after six days. He doesn't try giving Senna one, which kind of frightens David. It turns out that, because she's a witch, her heart is so hard that it would need to be replaced by a diamond. Nidhoggr was just being cheap.
- In Magic: The Gathering, Karn was created with a Phyrexian heartstone, which worked until he gave up his Planeswalker spark to help mend time rifts on Dominaria. When he did, the oil in the heartstone gradually corrupted him. During the Phyrexian takeover of Mirrodin, the Phyrexians attempted to convert him into their new Father of Machines. Ultimately subverted: his heartstone was replaced with Venser's human heart, restoring his Planeswalker spark and cleansing him of the Phyrexian corruption.
- Buzzjewels in Spelljammer. They're swarming insects that resemble large (hand-sized) dragonflies, which graze on "interesting" minerals like gemstones and eventually crystallize some sort of a small gem in their bellies, with a mildly poisonous bite to use if the swarm is attacked.
- Vis in Ars Magica, crystallized magic energy, often found coalesced in the magically potent parts of a beast. While not always strictly a gemstone (as the shape it takes is dictated by the storyguide's discretion and the particulars of any individual mage's magic), it often is. A dragon's heart is worth sixty pawns' worth. (To the uninitatied: it's a goddamn fortune.)
- A quite literal example from Tenra Bansho Zero: the "heart engines" powering the Humongous Mecha of the setting each contain the actual heart of one of the native Oni people, who are widely (and largely incorrectly) considered savage monsters by the local humans. Perhaps needless to say, this little secret is not something the people in the know feel exactly inclined to share with the general populace.
- In Dragon Quest VIII, the party has to go on a Matchmaker Quest on the behalf of the Prince of Argonia, who needs to slay an Argon Lizard and harvest their hearts as a sign of his coming of age and the right to marry Princess Medea of Trodain (who, unknown to him, has been transformed into a white mare due to a curse). Unfortunately, this person happens to be Prince Charmles, who is the epitome of entitled bastardry. And to make things worse, after you slay a Great Argon Lizard and do the hard work for him, Prince Charmles buys a larger (and presumably fake) Argon Heart from a shady merchant anyway! Son of a... Luckily, this comes back to bite him in the ass hard, costing him Medea and his undeserved sense of entitlement.
- Part of the backstory for Myst V: End of Ages reveals that this is true of the Laki, which appear to be something like otherworldly narwhals. The Laki collect gemstones in their gizzards to help them digest, and (before the cities in their world were destroyed by plague) were hunted almost to extinction in gladiatorial games to harvest them. They survived, but they don't get close enough to for the player to interact with them.
- In Legend of Mana, part of the Mana series, there are a race of humans called "Jumi" who all have some sort of precious gem in their chest. If it gets damaged, they could die.
- Deoxys from Pokémon Ruby and Sapphire. That gem on its chest is actually its brain.
- As the primary method of obtaining exotic crafting materials in Monster Hunter is carving them out of the steaming carcasses of giant monsters, this is both a present trope and driving motivation in the game. Aside from somewhat mundane materials, such as pelts or bones, some larger monsters outright have some organs identified ingame as gems. In addition to the internal organs, some truly massive beasts can also provide minerals by mining their hard outer carapaces.
- Heartcore: The titular item, Heartcores, are crystals that can be found in almost any living creature that possesses a heart, harvested by using demonic magic against the being who's heart you want to tear out. It serves as the main food source for demons as well as a mighty powerboost that can make the consumer stronger when eaten. They are incredibly valuable if they come from either humans or beastman, leading to demon being willing to start entire wars and genocides to get their hands on them. They also serve as a demons weakspot, since they all have these instead of hearts and the only way to kill a demon is to either destroy the head or the heartcore.
- The Gems of Steven Universe appear to be multicolored space babes with a magical gemstone somewhere on their bodies. In fact, they are magical gemstones, and their humanoid forms are merely constructs used to interact with the world. As such, they can regenerate from any injury given enough time, but damage to the Gem itself is life-threatening.
- In a less epic vein, oysters, and the pearls they generate. For a long time this was thought to be caused by grit in the shell, but this has long since been scientifically proven false, the pearl actually forms around parasites and worms inside the oyster, which it forms in order to contain them. There's even one particularly famous pearl with a fish skeleton as its core. The idea that pearls form around sand grains still pops up a lot in media.
- A more tragic example: The value of elephant-tusk ivory and rhinoceros horn (considered an aphrodisiac in some cultures) has led to both creatures being hunted to near-extinction.