Instinctive behaviours, such as hunting and defense, are part of the natural repertoire of behaviours that are shaped by evolution and critical for the survival of both individual and species. The midbrain periaqueductal gray (PAG) has emerged as a bottleneck in the routing of most instinctive behaviours, translating sensory and cognitive information into an appropriate motor response. Yet, the exact mechanisms of this translation remain elusive. We aimed to identify the neural circuits in the brainstem bridging the initiation and execution of instinctive behaviours in mice by developing an anatomical projection atlas of the PAG to downstream targets relevant for motor execution. To achieve this, we have analysed the synaptic connectivity of the PAG in a column- and cell type-specific manner using anterograde and retrograde viral tracing and whole brain fluorescence imaging. We describe a spatially-organised separation of downstream projection targets, as well as prominent cell type differences in long-range and local projection patterns. These anatomical differences support a spatial (and columnar) division of PAG ensembles and suggests separate processing pathways for different instinctive behaviours. Mapping the anatomical circuitry underlying multiple instinctive behaviours will ultimately guide further analyses of the neural mechanisms underlying instinctive behaviour output.