Introduction: In this study, we investigated the influence of in vivo disease pathology (measured as magnetic resonance imaging (MRI) lesion load and brain volume reduction) on cognitive functioning, especially the speed of processing, in multiple sclerosis (MS) patients. Since MS is characterized by cognitive slowing rather than impaired accuracy, we used the Amsterdam Neuropsychological Tasks (ANT) program, a computerized test proven to be very sensitive to cognitive slowing in MS patients. Methods: Thirty-two patients performed the ANT and underwent MRI scanning. Using the ANT computerized tests, we investigated focused, divided, sustained attention, executive function and psychomotor function, and examined associations of speed, speed fluctuation and accuracy of performance of these tests with MRI lesion load and brain volume parameters. Results: A decrease in the speed of processing and response speed stability, and a decrease in psychomotor accuracy and stability were clearly associated with less brain volume, and with higher lesion loads, in particular at frontal and occipital areas. Correlations with brain volume reduction were found for all domains, except for visuo-spatial processing. In particular, speed and speed fluctuation scores correlated with brain volume reduction, while accuracy of performance, in general, did not correlate. Only some test speed scores and speed fluctuation scores correlated with lesion load measurements. Conclusion: This study shows that, in MS patients, accuracy of processing is not compromised unless high working memory demands are involved. Problems in neurocognitive functioning in MS are mainly modulated by speed and stability of speed processing, in particular when attention-demanding controlled information processing is required. Abnormalities in these domains are most strongly associated with brain volume loss, confirming that pathology beyond focal lesions is important in MS.