Pain and temperature have a special role in the sense of bodily alert and consciousness, as they report information that has direct survival value. That is, since this information pertains to our physiological integrity, or threat to the integrity, their signals have evolutionarily acquired inherent value. How such information is used to guide general learning and decision-making as homeostatic signals, is well studied. However, we know much less about how pain and temperature learning reflect the topography of the body. Here, I will describe two combined behavioural and neuroimaging (fMRI) studies that show how different types of learning are anatomically specific. The first is in Pavlovian pain learning, where I will show evidence that a cerebellar system learns limb-specific conditioned responses. Importantly, this appears to be distinct from the well-known amygdala-dependent aversive learning system, which ignores anatomical specificity, and shows that multiple learning mechanisms underlie aversive conditioning. Second, in a perceptual learning paradigm, we show that experience-dependent improvements in temperature discrimination appear to be anatomically (laterality) specific. However, the brain laterality of this system is much less clear. Together, these findings show that both perceptual and motivational learning in the pain and temperature system incorporate mechanisms that retain basic anatomical specificity.