Neural synchrony between the subthalamic nucleus (STN) and cortex is critical for proper information processing in basal ganglia circuits. Using in vivo extracellular recordings in urethane-anaesthetized mice, we demonstrate that single units and local field potentials from the STN exhibit oscillatory entrainment to low-frequency (0.5-4Hz) rhythms when the cortex is in a synchronized state. Here we report novel findings in the R6/2 transgenic mouse model of Huntington's disease (HD) by demonstrating that STN activity is reduced and less phase-locked to cortical low-frequency oscillations. The spectral power of low-frequency oscillations in ECoG recordings of R6/2 mice is diminished while the spectral power of higher frequencies is augmented and such altered cortical patterning could lead to decreased synchrony in corticosubthalamic circuits. Our data establish that cortical entrainment of STN neural activity is disrupted in R6/2 mice and may be one of the mechanisms contributing to disordered motor control in HD. Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder in which impairments in the processing of information between the cortex and basal ganglia are fundamental to the onset and progression of the HD phenotype. The corticosubthalamic hyperdirect pathway plays a pivotal role in motor selection and blockade of neuronal activity in the subthalamic nucleus (STN) results in a hyperkinetic movement syndrome, similar to the HD phenotype. The aim of the present study was to examine the relationship between neuronal activity in the STN and cortex in an animal model of HD. We performed in vivo extracellular recordings in the STN to measure single-unit activity and local field potentials in the R6/2 transgenic mouse model of HD. These recordings were obtained during epochs of simultaneously acquired electrocorticogram (ECoG) in discrete brain states representative of global cortical network synchronization or desynchronization. Cortically patterned STN neuronal activity was less phase-locked in R6/2 mice, which is likely to result in less efficient coding of cortical inputs by the basal ganglia. In R6/2 mice, the power of the ECoG in lower frequencies (0.5-4Hz) was diminished while the power expressed in higher frequencies (13-100Hz) was increased. In addition, the spontaneous activity of STN neurons in R6/2 mice was reduced and neurons exhibited a more irregular firing pattern. Glutamatergic STN neurons provide the major excitatory drive to the output nuclei of the basal ganglia and altered discharge patterns could lead to aberrant basal ganglia output and disordered motor control in HD.