Joint position error (JPE) is frequently used to assess proprioception in rehabilitation and sport science. During position-reposition tests the subject is asked to replicate a specific target angle (e.g. 30° of knee flexion) for a specific number of times. The aim of this study is to find an effective method to estimate JPE from the joint kinematic signal. Forty healthy subjects were tested to assess knee joint position sense. Three different methods of JPE estimation are described and compared using a hierarchical clustering approach. Overall, the 3 methods showed a high degree of similarity, ranging from 88% to 100%. We concluded that it is preferable to use the more user-independent method, in which the operator does not have to manually place "critical" markers.