Objective. To present a method to determine the position and orientation of the mean optimal flexion axis of the elbow in vivo to be used in clinical research. Design. Registering the movements of the forearm with respect to the upper arm during five cycles of flexion and extension of the elbow using a 6 degrees-of-freedom electromagnetic tracking device. Background. Lessening of elbow endoprostheses could be caused by not placing the prostheses in a biomechanically optimal way. To evaluate the placement of endoprostheses with regard to loosening, a method to determine the elbow axis is needed. Methods. The movements of the right forearm with respect to the upper arm during flexion and extension were registered with a 6 degrees-of-freedom electromagnetic tracking device. A mean optimal instantaneous helical axis of 10 elbows was calculated in a coordinate system related to the humerus. Results. The average position of the flexion/extension axis was 0.81 cm (SD 0.66 cm) cranially and 1.86 cm (SD 0.72 cm) ventrally of the epicondylus lateralis. The average angle with the frontal plane was 15.3°(SD 2°). Conclusions. A useful estimation of the position and orientation of a mean optimal flexion axis can be obtained in vivo.