The intrinsic circuitry of the motor cortex comprises a complex network of connections whose synaptic relationships are poorly understood. This study was designed to determine the characteristics of subsets of GABAergic neurons containing the calcium-binding proteins parvalbumin (PV) and calbindin (CB), and their relationships with intrinsic axons in motor cortex. Immunohistochemically identified PV-containing neuronal profiles were more evenly distributed across cortical laminae (38% in II-III, 32% inV, 30% in VI) and more numerous (2.1/1) than CB-containing neuronal profiles (71% in II-III, 17% in V, 12% in VI). Relationships between neurons and axons intrinsic to motor cortex were visualized with fluorescent markers using the laser scanning confocal microscope. Similar percentages of PV (43%) and CB-immunoreactive (IR) (40%) neurons formed sparsely distributed appositions (1-5/neuron) with anterogradely labeled axons. The mean distances of such appositions from the somata were significantly different for the two groups (PV, mean = 22 microm, range = 1.6-93 microm; CB, mean = 32 microm, range = 6.2-132 microm). PV-IR neurons had a lower ratio of axosomatic/axodendritic appositions (1/99) compared with CB-IR neurons (14/86). Ultrastructural studies confirmed these findings. Fifty-seven percent of CB-IR neurons and 38% of PV-IR neurons formed synapses with intrinsic axons. Both populations received sparse input (1-6 synapses/neuron). Nearly all appositions between labeled terminals and postsynaptic profiles formed one synapse. Postsynaptic dendrites of PV-IR neurons (mean = 1.4 microm diameter) were larger than those of CB-IR neurons (mean = 1.1 microm), indicating more proximal synapses. Distinct input patterns of intrinsic axons to the two populations of neurons suggest unique roles in cortical processing.