In this study, we evaluated persistent cognitive deficits in whiplash injury (WI) patients and compared these to cognitive functioning in mild traumatic brain injury (MTBI) patients and healthy controls (HC). Sixty-one patients suffering from a WI were compared with 57 patients suffering from a MTBI and with 30 HC. They were examined with an extensive neuropsychological test battery assessing attention, memory, and visuospatial and executive functions. In both patient groups, participants showed persistent cognitive symptoms (more than 6 months post-injury). The two patient groups did not differ significantly with regard to measurements of attention, memory, and visuospatial and executive functions. The WI group, as compared to the HC group, was found to be significantly more deficient in speed of performance during sustained and divided attention, focused attention, alternating attention, the storage of new auditory-verbal unrelated information into memory, the long-term delayed recall of stored auditory-verbal related information from memory, abstract reasoning and accuracy of performance during planning and problem solving. No differences could be found between both groups concerning speed of information processing, visuospatial abilities and verbal fluency.