Assessment of upper extremity motor skills often involves object manipulation, drawing or writing using a pencil, or performing specific gestures. Traditional assessment of such skills usually requires a trained person to record the time and accuracy resulting in a process that can be labor intensive and costly. Automating the entire assessment process will potentially lower the cost, produce electronically recorded data, broaden the implementations, and provide additional assessment infor-mation. This paper presents a low-cost, versatile, and easy-to-use algorithm to automatically detect and track single or multiple well-defined geometric shapes or markers. It therefore can be applied to a wide range of assessment protocols that involve object manipulation or hand and arm gestures. The algorithm localizes the objects using color thresholding and morphological operations and then estimates their 3-dimensional pose. The utility of the algorithm is demonstrated by implementing it for automating the following five protocols: the sport of Cup Stacking, the Soda Pop Coordination test, the Wechsler Block Design test, the visual-motor integration test, and gesture recognition.