Attempts were made to determine the afferent and efferent connections of the subthalamic nucleus (STN) in the monkey using retrograde and anterograde axoplasmic transport technics. Following HRP injections limited to the STN, label was transported to arrays of cells adjacent, and parallel, to the lateral medullary lamina in the rostral two thirds of the lateral pallidal segment (LPS). Only sparse label was transported to cells of the pedunculopontine nucleus (PPN) and the locus ceruleus (LC). No enzyme was transported across the midline, or to the striatum, medial pallidal segment (MPS), thalamus, substantia nigra (SN) or dorsal nucleus of the raphe (DNR). HRP injected into portions of both the STN and SN produced retrograde transport of the enzyme to cells in parallel arrays in the LPS related rostrocaudally to the injection site. Additional enzyme transport was seen in cells of the striatum, the DNR and the PPN. Only a few isolated cells were labeled in the sensorimotor cortex. Efferent connections of the STN were studied in monkeys in which [3H]amino acids were injected hydraulically or iontophoretically into the STN. Isotope traced in serial autoradiographs was distributed to: (1) both segments of the globus pallidus (GP) in arrays parallel to the medullary laminae, and (2) the pars reticulata of SN (SNpr). The greatest number of terminals was found in the MPS. Fibers from the rostral part of the STN descended along the dorsal border of the SN and projected ventrally to terminations in the SNpr. No isotope was transported across the midline, or to the striatum, thalamus, DNR or PPN. Isotope injected into both the STN and SN produced similar transport to the GP and transport via nigral efferent fibers to: (1) portions of the striatum, (2) specific thalamic nuclei (VAmc, VLm, DMpl), (3) deep and middle gray layers of the superior colliculus and (4) PPN. Control studies indicated that [3H]amino acids injected only into the SN were transported to PPN. HRP injected into PPN produced profuse retrograde transport in cells of the MPS and SNpr and distinct label in a few cells of the zona incerta and STN. These data suggest that the STN receives its major subcortical input from cell of the LPS arranged in arrays which have a rostrocaudal organization. No cells of the MPS or SN project to the STN. The output of the STN is to both segments of the GP and SNpr. Major subcortical projections to PPN arise from the MPS and SNpr, but afferents also arise from other sources. The major projection of PPN is to SN.