The bony plates along the back of Stegosaurus have no clear modern analogue, and their function defies any easy explanation. They clearly evolved from more obviously protective spikes that lined the back in less derived stegosaurs, and perhaps they served a similar function in Stegosaurus. Their wide, thin shape hints at additional possibilities, however. The fact that these structures would have appeared to increase the height of the animal suggests that they were display structures used to intimidate enemies or impress potential mates.

Also, Stegosaurus plates are lined with grooves that once housed blood vessels, leading James Farlow, Carl Thompson and Daniel Rosner to suggest that they served a thermoregulatory function, providing surface area to dissipate internal heat. As warm blood flowed from the body through the plates, wind blowing across the plates would cool the blood before it returned to the body, providing a sort of biological air conditioning. Possibly the plates functioned in all these respects.

At the end of the tail,Stegosaurus stenops had four spikes pointing laterally (to the side), a structure referred to as a Thagomizer, after a Far Side cartoon where the structure was first named "in memory of [unfortunate caveman] Thag Simmons." It is universally considered a means of defense, a weapon that could seriously injure any attacker. The four-spiked thagomizer is not a universal character in all stegosaurs, the species Stegosaurus ungulatus has eight spikes, and the African genus Kentrosaurus had fourteen spikes running from the lower back to the tip of the tail.