A fundamental scientific goal in auditory neuroscience is identifying what mechanisms allow the brain to transform an unlabeled mixture of auditory stimuli into distinct perceptual representations. This transformation is accomplished by a complex interaction of multiple neurocomputational processes, including Gestalt grouping mechanisms, categorization, attention, and perceptual decision-making. Despite a great deal of scientific energy devoted to understanding these principles of hearing, we still do not understand either how auditory perception arises from neural activity or the causal relationship between neural activity and auditory perception. Here, we review the contributions of cortical and subcortical regions to auditory perceptual decisions with an emphasis on those studies that simultaneously measure behavior and neural activity. We also put forth challenges to the field that must be faced if we are to further our understanding of the relationship between neural activity and auditory perception.