A method is presented for extraction of intra and inter fraction motion of seeds/markers within the patient from cone beam CT (CBCT) projection images. The position of the marker is determined on each projection image and fitted to a function describing the projection of a fixed point onto the imaging panel at different gantry angles. The fitted parameters provide the mean marker position with respect to the isocentre. Differences between the theoretical function and the actual projected marker positions are used to estimate the range of intra fraction motion and the principal motion axis in the transverse plane. The method was validated using CBCT projection images of a static marker at known locations and of a marker moving with known amplitude. The mean difference between actual and measured motion range was less than 1 mm in all directions, although errors of up to 5 mm were observed when large amplitude motion was present in an orthogonal direction. In these cases it was possible to calculate the range of motion magnitudes consistent with the observed marker trajectory. The method was shown to be feasible using clinical CBCT projections of a pancreas cancer patient.