Behavioral arrest is an essential feature of an animal's survival. Acoustic startle reflex (ASR) is an involuntary whole-body contraction of the skeletal musculature to an unexpected auditory stimulus. This strong reaction can be decreased by prepulse inhibition (PPI) phenomenon; which, for example, is important in reducing distraction during the processing of sensory input. Several brainstem regions are involved in the PPI and startle reflex, but a previous study from our laboratory showed that the main input structure of Basal Ganglia (BG) - the striatum - modulates PPI. The pallidum and nigra are connected with striatum and these brainstem structures. Here, we investigated the role of these striatum outputs in the brain regions on startle amplitude, PPI regulation, and exploratory behavior in Wistar rats. The temporary bilateral inhibition of the globus pallidus (GP) by muscimol lead to motor impairment, without disturbing startle amplitude or PPI. Similarly, inhibition of the entopeduncular nucleus (EPN) specifically disrupted the exploratory behavior. On the other hand, the substantia nigra reticulata (SNr) inhibition interfered in all measured behaviors: decreased the PPI percentage, increased ASR and impaired the locomotor activity. The nigra is a key BG output structure which projects to the thalamus and brainstem. These findings extend our previous study showing that the striatum neurons expressing D1 receptors involvement in PPI occurs via the direct pathway to SNr, but not to the pallidum which more likely occurs by its connection with the caudal pontine nucleus, superior colliculus and/or pedunculopontine nucleus pivotal structures for startle reflex modulation. Copyright © 2019 Elsevier Ltd. All rights reserved.