The prefrontal cortex projects to many thalamic nuclei, in pathways associated with cognition, emotion, and action. We investigated how multiple projection systems to the thalamus are organized in prefrontal cortex after injection of distinct retrograde tracers in the principal mediodorsal (MD), the limbic anterior medial (AM), and the motor-related ventral anterior/ventral lateral (VA/VL) thalamic nuclei in rhesus monkeys. Neurons projecting to these nuclei were organized in interdigitated modules extending vertically within layers VI and V. Projection neurons were also organized in layers. The majority of projection neurons to MD or AM originated in layer VI ( approximately 80%), but a significant proportion ( approximately 20%) originated in layer V. In contrast, prefrontal neurons projecting to VA/VL were equally distributed in layers V and VI. Neurons directed to VA/VL occupied mostly the upper part of layer V, while neurons directed to MD or AM occupied mostly the deep part of layer V. The highest proportions of projection neurons in layer V to each nucleus were found in dorsal and medial prefrontal areas. The laminar organization of prefrontal cortico-thalamic projections differs from sensory systems, where projections originate predominantly or entirely from layer VI. Previous studies indicate that layer V cortico-thalamic neurons innervate through some large terminals thalamic neurons that project widely to superficial cortical layers. The large population of prefrontal projection neurons in layer V may drive thalamic neurons, triggering synchronization by recruiting several cortical areas through widespread thalamo-cortical projections to layer I. These pathways may underlie the synthesis of cognition, emotion and action.