Your vertebrae have little shock-absorbers on either side called [facet joints](https://en.wikipedia.org/wiki/Facet_joint), little capsules of cartilage filled with a lubricant called [synovial fluid](https://en.wikipedia.org/wiki/Synovial_fluid). They keep your neck from moving in ways that would be harmful to your spinal cord, and keep your vertebrae from wearing down due to bone-on-bone friction.
If you intentionally stretch them you decrease the pressure in them enough to make bubbles of nitrogen come out of the synovial fluid. This sudden decrease in pressure allows your neck to stretch more, which often feels good even as it makes horrible sounds. The bubbles can happen even in regular movement, so in general they aren’t harmful; they either get off-gassed or reabsorbed.
These are the same bubbles that occur if you get ‘[the bends](https://en.wikipedia.org/wiki/Decompression_sickness)’ from spending too much time diving and too little time decompressing, compensating for the differences in pressure at different depths. This usually manifests first as joint pain as too many bubbles boil out of the fluid, increasing the pressure in your joints.
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