The discoveries of coding principles of vision, olfaction, gustation, audition, and somatosensation are all landmark achievements. However, principles defining how the brain processes signals from visceral organs to generate internal senses remain largely unknown. We developed a novel brainstem calcium imaging platform. Using this system, we report that the brainstem uses discrete neuronal populations to encode different organs and combinatorial codes for different mechano- and chemosensory modalities in the same organ. Furthermore, organs are topographically mapped in the brainstem, forming a “visceral homunculus”. The spatial map in the brain arises from distributed representations in the sensory ganglia and depends on local inhibition. This publication provides the first analysis of the logic used by the brain to process interoceptive inputs. In addition, our study helps define the wide-open field of viscerosensory coding, laying the foundation for future work to comprehend the neural processing of bodily signals throughout the brain.