The Fugl-Meyer Assessment (FMA) is a widely used evaluation tool for assessing upper extremity motor function during stroke rehabilitation. However, the FMA is a repetitive, time-consuming task that currently must be performed by therapists in a hospital or clinic. We thus propose an alternative automated approach in which patients perform FMA movements while holding a cellphone at the hand and receive automated FMA scores. In the proposed system, features are extracted from cellphone movement data and decision trees are used to automatically score FMA test items. Ten stroke patients with upper extremity dysfunction participated in a validation experiment to compare automated FMA scores with traditional FMA scores from a trained therapist. Results showed that FMA scores from the cellphone-based automated system were highly correlated with FMA scores from the trained therapist (r2 = 0.97), and that the average accuracy for individual FMA test items was 85%. These results demonstrate that such a portable, automated FMA system could potentially be used to assess upper extremity function during stroke rehabilitation to remove the repetitive, time-consuming burden from therapists and could potentially be performed in clinic or home-based settings.