Projections from the claustrum (Cl) and the thalamic anterior intralaminar nuclei (AIN) to different representations within the primary somatosensory (S1) and visual (V1) areas were studied using the multiple retrograde fluorescent tracing technique. The injected cortical regions were identified electrophysiologically. Retrograde labeling in Cl reveals two different projection patterns. The first pattern is characterized by a clear topographic organization and is composed of two parts. The somatosensory Cl shows a dorsoventral progression of cells projecting to the hindpaw, forepaw, and face representations of S1. The visual Cl has cells projecting to the vertical meridian representation of V1 surrounded dorsally by neurons projecting to the representation of retinal periphery. A second pattern of Cl projections is composed of neurons that are distributed diffusely through the nucleus. In both somatosensory and visual sectors, these intermingle with the topographically projecting cells. Neurons retrogradely labeled from cortical injections are always present in the AIN. In the central medial nucleus, the segregation of modality is evident: The visual-projecting sector is dorsal, and the somatosensory is ventral. Projections from the central lateral nucleus display detectable somatotopic and retinotopic organization: Individual regions are preferentially connected with specific representations of S1 or V1. In the paracentral nucleus, no clear regional preferences are detectable. Also performed were comparisons of the proportions of neurons projecting to different sensory representations. Projections to V1 from both AIN and Cl are biased towards the retinal periphery representation. S1 projection preference is for the forepaw representation in Cl and for the hindpaw in the AIN. The quantitative analysis of multiply labeled cells reveals that, compared to Cl, the AIN contains a higher proportion of neurons branching between different representations of S1 or V1. The concept of topographic vs. diffuse projecting systems is reviewed and discussed, and functional implications of quantitative analysis are considered.