Structural alterations of the basal ganglia occur in patients with Huntington's disease (HD). The aim of this exploratory study was to assess auditory processing mechanisms by functional MRI (fMRI) in patients with premanifest (pHD) and manifest HD to gain more insight in possible alterations in basal ganglia–thalamic circuits. Sixteen HD and 18 pHD as well as corresponding age- and gender-matched controls were included. The pHD group was divided into two subgroups close (cpHD; <10 years) and far pHD (fcHP; >10 years), according to their estimated age of disease onset (eAO). Tone perception and processing were visualized by 3T fMRI by employing repeated tone stimulation through digitally generated pulsed (ν=5Hz) 800-Hz sine tones. We found altered activation in basal ganglia–thalamic circuits in HD and/or pHD compared to controls. (i) The cpHD group presented predominantly down-regulated processes compared to fpHD and HD. (ii) HD presented stronger bilateral activation of the putamen and (iii) fpHD presented stronger bilateral activation of the thalamus and also right caudatum. (iv) Depending on the progress of the disease, a shift towards the activation of more right hemispherical areas can be observed. Our findings seem to reflect an altered activation pattern to auditory stimulation depending on the progression of neuronal dysfunction in HD and pHD. They also stress the involvement of the basal ganglia–thalamic circuits in the processing of sensory auditory stimuli.