Tourette's syndrome and Huntington's disease have long been clinically associated with attentional deficits. In this study, we aimed to determine the nature and quantify the extent of such deficits. A technique was devised to ascertain the efficiency with which Tourette's syndrome and Huntington's disease patients could shift and direct attention away from naturally expected stimulus-response (S-R) linkages. This was done by varying the relationships formed between stimulus and response location. Attentional efficiency was indicated by relative speed of responding to relevant (congruent) and irrelevant (incongruent) stimuli, in a paradigm developed from the Simon effect. There were five conditions progressively increasing in complexity. The stimuli consisted of left and right pointing arrows and, in some cases, various conditionality manipulations were also employed, such that in the presence of a certain symbol (i.e. 'x') the nature of the response had to be reversed, whereas in the presence of an alternative symbol (i.e. '='), the response was compatible with the direction of the arrow. As predicted, Tourette's syndrome and Huntington's disease patients, regardless of medication or depression status and unlike controls, were particularly disadvantaged in responding to various conflicting S-R configurations. Tourette's syndrome and Huntington's disease patients may experience difficulties in making attentional shifts, or in inhibiting inappropriate responses; they may also be more susceptible (than controls) to the conflict that can arise when the spatial code formed for the stimulus is irrelevant for selecting the appropriate response. We conclude that our findings support the notion that cognitive deficits in Tourette's syndrome and Huntington's disease may stem from abnormalities of the major pathways interconnecting the basal ganglia and the frontal lobes.