Understanding the foundations of the neurobiology of behavior and well-being can help us better achieve animal welfare. Behavior is the expression of several physiological, endocrine, motor and emotional responses that are coordinated by the central nervous system from the processing of internal and external stimuli. In mammals, seven basic emotional systems have been described that when activated by the right stimuli evoke positive or negative innate responses that evolved to facilitate biological fitness. This review describes the process of how those neurobiological systems can directly influence animal welfare. We also describe examples of the interaction between primary (innate) and secondary (learned) processes that influence behavior.