Godzilla's signature weapon is his distinctive atomic breath. Godzilla's dorsal fins glow blue and white ominously, and then he lets loose with a concentrated blast of radiation from his mouth. This power is commonly mistaken for breathing literal fire. He has defeated Mothra, the Kamakiras, and Hedora with his radiation beam.

Godzilla has been shown apparently being able to adjust the intensity of his ray, varying from a blast of superheated vapour (such as in the 1950s and 1960s), to a beam with explosive and kinetic properties, (in the 1970s and onward.) The ray is usually portrayed as being neon blue, though in Godzilla 2000 and Godzilla vs. Megaguirus, it is a reddish orange.

In Godzilla vs. Megaguirus the ray was shown to have incredible incendiary properties and was powerful enough to destroy a miniature black hole, while in Godzilla: Final Wars, it possessed incredible range, amazing power and pin-point accuracy, able to hit a target in outer space and kill most kaiju with a single shot. In a memorable (and somewhat infamous) scene in Godzilla vs. Hedorah, Godzilla even used his atomic breath to fly by aiming it at the ground and lifting off like a rocket.

A variation of the standard atomic ray in the Heisei series was the red "spiral ray" that he acquired as a result of absorbing the Rodan's life energy. This ray was so powerful that only a few blasts of it were sufficient to completely destroy Mechagodzilla and SpaceGodzilla. Destoroyah was able to withstand several hits of the "spiral ray."

In GMK, a variant of his spiral ray was seen when King Ghidorah used his golden gravity beams on Godzilla. Godzilla was somehow able to draw strength from the gravity beams and used the absorbed energy to fire a blast of blue energy wrapped in a golden spiral that completely destroyed Ghidorah. The spiral ray returned in Godzilla: Final Wars, where it was strong enough to push Kaiser Ghidorah into the atmosphere, destroying him in an explosion visible from the surface of the earth.