Introduction: Nigrothalamocortical tract is one of the important outputs of the basal ganglia, but its role in motor disturbances is still vauge, beacause there is little informations on its connection structure. Some electrophysiological and pharmacological studies report that non-dopaminergic outputs originate from reticular part of substatia nigra to thalamus. In this study the topographical and organization connection of substantia nigra pars reticulata (SNR) with thalamic MD nucleus was investigated using HRP tracer. Materials and Methods: 25 male rats received injection of 33% HRP into the ipsilateral MD nucleus of thalamus stereotaxically. 48 hours later the animals were perfused transcardially, and the brain tissue was fixed. 40 micrometer sections were prepared from diencephalon and midbrain. Following enzymatic reactions of TMB, the sections were stained by neutral red. Results: The light microscopic study showed that there is a high concentration of neurons which project to the MD nucleus from the rostro-lateral part and middle parts of pars reticulata (SNR) and the number of labeled cells decrease in the caudal parts. Other labeled neurons are located at the border of SNC, SNR and VTA, specially close to the passage of III cranial nerve. In general, the size of neurons was mostly medium; and they were multipolar in shape. Any labeled cells were observed in the SNR controlateral to injection site. Conclusion: Our findings show that the SNR connection to the MD arises mainly from lateral and dorsomedial part of SNR. It seems that these connection may influence the limbic system in orientating behavior.