Three-dimensional atlases of subcortical brain structures are valuable tools to reference anatomy in neuroscience and neurology. In the special case of deep brain stimulation (DBS), the three most common targets are the subthalamic nucleus (STN), the internal part of the pallidum (GPi) and the ventral intermediate nucleus of the thalamus (VIM). With the help of atlases that define the position and shape of these target regions within a well- defined stereotactic space, their spatial relationship to implanted deep brain stimulation (DBS) electrodes may be determined. Here we present a composite atlas based on manual segmentations of a multi-modal high- resolution MNI template series, histology and structural connectivity. To attain exact congruence to the template anatomy, key structures were defined using all four modalities of the template simultaneously. In a first step tissue probability maps were defined based on the multimodal intensity profile of each structure. These observer-independent probability maps provided an excellent basis for the subsequent manual segmentation particularly when defining the outline of the target regions. Second, the key structures were used as an anchor point to coregister a histology based atlas into standard space. Finally, a sub-segmentation of the subthalamic nucleus into three functional zones was estimated based on structural connectivity. The resulting composite atlas uses the spatial information of the MNI template for DBS key structures that are visible on the template itself. For remaining structures, it relies on histology or structural connectivity. In this way the final atlas combines the anatomical detail of a histology based atlas with the spatial accuracy of key structures in relationship to the template anatomy. Thus, the atlas provides an ideal tool for the analysis of DBS electrode placement.