OBJECTIVE: In cognitive neuroscience, well-controlled and highly specific paradigms have been developed to measure cognitive processes over the last decades, often using computer-assisted presentation and response registration. This approach is in contrast with the traditional paper-and-pencil tests used in clinical neuropsychology, which typically assess cognitive function in a less specific manner, often even at the level of a cognitive domain. As a result, important aspects of cognitive (dys)function may be missed during a neuropsychological assessment. This paper focuses on the main challenges that need to be overcome in order to successfully integrate experimental paradigms from cognitive neuroscience into the clinical practice of neuropsychologists. METHOD: Six challenges are discussed: (i) experimental paradigms are often lengthy and may be overly specific; (ii) technical limitations even today hamper their application in clinics; (iii) the psychometric properties of methods used in cognitive neuroscience are under-examined or poor; (iv) many paradigms from cognitive neuroscience rely on reaction times rather than accuracy, limiting their use in the many brain-injured patients with processing speed deficits; (v) the predictive and ecological validity of these paradigms often unclear; (vi) technological progress (e.g. Moore's law) seriously affects the continuous availability of experimental computerized assessment methods. CONCLUSION: Both cognitive neuroscientists and clinical neuropsychologists should work together to develop and validate novel paradigms for use in clinical assessments that are platform-independent, reliable and valid, user friendly and easy to use in clinical practice.