Pyramidal cells in the neocortex are differentiated into several subgroups based on their extracortical projection targets. However, little is known regarding the relative intracortical connectivity of pyramidal neurons specialized for these specific output channels. We used paired recordings and quantitative morphological analysis to reveal distinct synaptic transmission properties, connection patterns, and morphological differentiation correlated with heterogeneous thalamic input to two different groups of pyramidal cells residing in layer 5 (L5) of rat frontal cortex. Retrograde tracers were used to label two projection subtypes in L5: crossed-corticostriatal (CCS) cells projecting to both sides of the striatum, and corticopontine (CPn) cells projecting to the ipsilateral pons. Although CPn/CPn and CCS/CCS pairs had similar connection probabilities, CPn/CPn pairs exhibited greater reciprocal connectivity, stronger unitary synaptic transmission, and more facilitation of paired-pulse responses. These synaptic characteristics were strongly correlated to the projection subtype of the presynaptic neuron. CPn and CCS cells were further differentiated according to their somatic position (L5a and L5b, the latter denser thalamic afferent fibers) and their dendritic/axonal arborizations. Together, our data demonstrate that the pyramidal projection system is segregated into different output channels according to subcortical target and thalamic input, and that information flow within and between these channels is selectively organized.