Flickr user modern_fred's Japanese movie monster scan collection includes a few vintage illustrations detailing the innards of Godzilla and other famous kaiju.
Godzilla
This anatomical sketch of Godzilla reveals a relatively small brain, giant lungs that allow underwater breathing, leg muscles that can support 20,000 tons of body weight, and a "uranium sack" and "nuclear reaction sack" that produce radioactive fire-breath and energize the body.
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Jiger reveals her inner self
According to this anatomical drawing, Jiger has a pair of horns that can shoot missiles made of hardened saliva and one that fires a deadly magnetium (?) beam.
Jiger (uploaded by Paulkaiju)
Other characteristics include extremely powerful suction cups covering the entire body, an organ that enables Jiger to spit jets of seawater at 300 kilometers per hour, a stomach that can melt iron ore, and a tail that functions as an ovipositor.
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Mothra larva
This anatomical sketch of Mothra in larval form shows a robust jaw, an enormous stomach, an elongated silk-producing organ, a row of breathing orifices on either side of the body, countless cilia on the bottom surface, and a rudimentary nervous system consisting of a cerebral ganglion and a network of nerve ganglia distributed across the body.
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Guiron -- a peek inside the belly of the beast
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Anguirus
This anatomical diagram of Anguirus shows eyes that can detect infrared light, a pair of sub-brains that control the forelegs and rear legs, highly developed rear leg muscles, and a heavily spiked rear carapace.
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This illustration of "Flaming Monster Gamera" (from An Anatomical Guide to Monsters) reveals eyes that can see in the dark, arms strong enough to lift and throw a 50-ton boat, and "fire sacks" that let Gamera shoot flames from his hands.
Gamera
The illustration also shows a series of sack-like organs for storing lava, oil, coal and uranium (like Godzilla), as well as balloon-like organs in the legs that can blast air through the bottoms of the feet.
[Link: modern_fred's kaiju eiga photoset]
Related: Kaiju art collection