Tourette syndrome (TS) is characterised by stereotyped involuntary movements, called tics. Some evidence suggests that structural and functional abnormalities of the basal ganglia may explain these motor symptoms. In this study, the probabilistic classification learning (PCL) test was used to evaluate basal ganglia functions in 10 children with less severe tics (Yale Global Tic Severity Scale (YGTSS) scores<30) and in 10 children with more severe symptoms (YGTSS score>30). In the PCL task, participants are asked to decide whether different combinations of four geometric forms (cues) predict rainy or sunny weather. Each cue is probabilistically related to a weather outcome, and feedback is provided after each decision. After completion of the probabilistic stimulus-response learning procedure, subjects received a transfer test to assess explicit knowledge about the cues. The children with TS exhibited impaired learning in the PCL task in comparison with the 20 healthy control subjects. This impairment was more pronounced in the TS patients with severe symptoms, and there was a significant negative relationship between the final classification performance and the YGTSS scores. The patients showed normal learning in the transfer test. These results suggest that the neostriatal habit learning system, which may play a central role in the acquisition of probabilistic associations, is dysfunctional in TS, especially in the case of more severe motor symptoms. The classification performance and the severity of tics were independent of the explicit knowledge obtained during the test.