Although there has been a resurgence in the field of canine cognition, little research has focused on the neural mechanisms that underlie perception in domestic dogs. In this dissertation, I argue that functional magnetic resonance imaging (fMRI) provides a key insight into the role of brain regions that support stimulus-reward associations and brain-based biases for specific stimulus modalities in domestic dogs. The question is how these neurobiological mechanisms drive perceptual learning and discrimination in dogs, and how this varies based on the stimulus modality. This question was approached in three manuscripts using awake fMRI of 19 pet dogs. The first manuscript assessed whether reward systems in the dog brain process the predictive value of salient stimuli regardless of their sensory modality, or if some sensory modalities are privileged over others. The neurobiological learning curves of BOLD activation over time were compared to assess whether the rates of stimulus-reward acquisition were modality-dependent. We found that stimulus-reward associations were formed at a faster rate for olfactory and visual stimuli over verbal stimuli in reward processing regions of the dog brain. The second manuscript investigated the neural mechanisms of word discrimination in dogs using an auditory oddball paradigm consisting of trained words versus novel pseudowords. Dogs had greater neural activation to novel pseudowords relative to trained words in auditory processing regions. Multivoxel pattern analysis (MVPA) further revealed that a subset of dogs had clusters of informative voxels that discriminated between the two trained words in regions analogous to language processing regions in humans. The third manuscript identified brain regions important for processing object stimuli. We asked whether dogs’ perception of objects is affected by a) the possible affordances dogs’ associate with an object and b) whether the object is presented as a 2D or 3D version. We found that dogs have neural biases for processing object stimuli that the dog can interact with using their mouth and for the stimulus dimension with which they are most familiar. Together, these studies inform our current understanding of how dogs perceive their environment.