Paroxysmal kinesigenic choreoathetosis (PKC) is a rare neurologic disorder characterized by sudden attacks of brief involuntary dyskinetic movement, which are precipitated by voluntary movement. The pathophysiology of PKC remains unclear. The purpose of this study is to localize cerebral functional abnormalities in idiopathic PKC with resting-state functional magnetic resonance imaging (fMRI). From May 2007 to August 2008, seven patients with idiopathic PKC were included. The mean age of onset was 11.7 +/- 3.1 (range, 8-17) years and the mean disease duration was 6.9 +/- 5.1 (range, 1-14) years. Seven subjects of an age- and sex-matched control group were recruited. Interictal brain fMRI was performed in the PKC patients and in the normal controls. Voxel-based analysis was used to characterize the alteration of amplitude of low frequency fluctuation (ALFF) in patients with PKC. Difference between the patient patterns and the control was analyzed with Student t-test. The whole brain analysis indicated that the patient group had significantly increased ALFF in the bilateral putamen (P < 0.005) than normal control. fMRI could be useful to evaluate PKC with negative conventional imaging. It was suggested that abnormal cortico-striato-pallido-thalamic loop might be associated with the pathophysiology of idiopathic PKC.