Although the amygdala complex is a brain area critical for human behavior, knowledge of its subspecialization is primarily derived from experiments in animals. We here employed methods for large-scale data mining to perform a connectivity-derived parcellation of the human amygdala based on whole-brain coactivation patterns computed for each seed voxel. Voxels within the histologically defined human amygdala were clustered into distinct groups based on their brain-wide coactivation maps. Using this approach, connectivity-based parcellation divided the amygdala into three distinct clusters that are highly consistent with earlier microstructural distinctions. Meta-analytic connectivity modelling then revealed the derived clusters’ brain-wide connectivity patterns, while meta-data profiling allowed their functional characterization. These analyses revealed that the amygdala’s laterobasal nuclei group was associated with coordinating high-level sensory input, whereas its centromedial nuclei group was linked to mediating attentional, vegetative, and motor responses. The often-neglected superficial nuclei group emerged as particularly sensitive to olfactory and probably social information processing. The results of this model-free approach support the concordance of structural, connectional, and functional organization in the human amygdala and point to the importance of acknowledging the heterogeneity of this region in neuroimaging research.