Quantitative assessment of motor performance is important for diseases of motor control, such as Parkinson's disease (PD). Manual tracking tasks are well suited for motor assessment, as they can be performed concomitantly with brain mapping techniques. Here we propose utilizing second-order linear dynamical systems to assess manual pursuit tracking performance. With the desired trajectory as the input, and the subject's actual motor response as the output, a linear model characterized by natural frequency and damping ratio is identified for each subject. We applied this method to 10 PD subjects (on and off L: -dopa medication) and 10 normal subjects performing a multi-frequency sinusoidal tracking task. Model parameters were more sensitive than overall tracking errors in determining significant differences between groups. The effect of L: -dopa medication was to reduce the damping ratio and make the range in natural frequency across individuals approach that of normal subjects. We interpret the changes in damping ratio and natural frequency as possibly related to suppression of compensatory cerebellar activity and/or improvement of motor program selection, and the changes in natural frequency as an implicit strategy to maintain settling time in the face of reduce damping ratio. Our results suggest that simple linear dynamical system models can be a powerful method to assess tracking performance in Parkinson's disease because of the additional insight they can provide into neurological processes.