The higher-order thalamus has an important role for cortico-thalamo-cortical information processing. A precise knowledge of the anatomical structure of thalamocortical projections is necessary to better understand this kind of information processing compared to direct cortico-cortical routes. Therefore, neurons in the thalamus of mice were retrogradely labelled by injecting cholera toxin subunit B conjugates into the primary somatosensory cortex and the motor cortex. The stained neurons were automatically detected in the microscopic images and then assigned to corresponding anatomical structures. Five higher-order thalamic nuclei were analysed in more detail afterwards. This revealed shared principles underlying the structure of thalamocortical projections: On the one hand, neurons followed a clear topographical arrangement in the thalamic nuclei. For example, within the posterior complex of the thalamus, more dorsally located cells projected to more anterior and more ventrally located cells to more posterior areas of the primary somatosensory cortex. On the other hand, cells with simultaneous projection to both cortical areas were found in all five thalamic nuclei by using co-injections. Such cells could transmit the same information to different cortical areas. These experiments can help to better understand the functional significance of cortico-thalamo-cortical networks.