BACKGROUND: Individuals with Substance Use Disorders (SUDs) have disruptions in the brain's dopaminergic (DA) system and the functioning of its target neural substrates (striatum and prefrontal cortex). These substrates are important for the normal processing of reward, inhibitory control and motivation. Cognitive deficits in attention, impulsivity and working memory have been found in individuals with SUDs and are predictors of poor SUD treatment outcomes and relapse in alcohol and cocaine dependence specifically. Furthermore, the DA system and accompanying neural substrates play a key role in the timing of motor acts (motor timing). Motor timing deficits have been found in DA system related disorders and more recently also in individuals with SUDs. Motor timing is found to correlate with attention, impulsivity and working memory deficits. To our knowledge motor timing, with regards to treatment outcome and relapse, has not been investigated in populations with SUDs. METHODS/DESIGN: This study aims to investigate motor timing and its relation to treatment response (at 8 weeks) and relapse (at 12 months) in cocaine and/or alcohol dependent individuals. The tested sensitivity values of motor timing parameters will be compared to a battery of neurocognitive tests, owing to the novelty of the motor task battery, the confounding effects of attention and working memory on motor timing paradigms, and high impulsivity levels found in individuals with SUDs. DISCUSSION: This research will contribute to current knowledge of neuropsychological deficits associated with treatment response in SUDs and possibly provide an opportunity to individualize and modify currently available treatments through the possible prognostic value of motor task performance in cocaine and/or alcohol dependent individuals.