Decades of research on the neurobiology of autism spectrum disorder (ASD) have generally overlooked the importance of co-occurring anxiety. This is surprising, as neurobiological accounts of ASD and anxiety disorders point to highly overlapping systems. This chapter describes the overlap between the neurobiology of anxiety and ASD, with a particular emphasis on amygdala function and structure. As we discuss, the successful integration of diverging patterns of amygdala activity in ASD and anxiety represents one of the biggest advances we could make in understanding their co-occurrence. This chapter also reviews the role of prefrontal cortex (PFC) in modulating amygdala function, and how differences in amygdala/PFC connectivity may influence the presentation of anxiety in ASD. Lastly, we review the overlap between anxiety, ASD, and peripheral nervous system function (heart rate, heart rate variability, and electrodermal activity). Key agendas for future research on anxiety in ASD include the validation of new, wireless technology for large-scale investigations of peripheral nervous system function, the increased use of experimental manipulations of anxiety, and an increased reliance on developmental perspectives.