Cutter runout is a common phenomenon affecting the cutting performances in milling operations. To date, most of the milling process models considering cutter runout were established based on the circular tooth path approximation, which brought errors into the runout estimation. In this paper, a new approach is presented for modelling the milling process geometry with cutter runout based on the true tooth trajectory of cutter in milling. The mathematical relationship between the trajectories generated by successive cutter teeth with runout is analysed. The milling process geometrical parameters, including the instantaneous undeformed chip thickness, the entry and exit angles of a cutting tooth, and the ideal peripheral machined workpiece surface roughness, are modelled according to the true tooth trajectories. Numerical method is used to solve the derived transcendental equations. A simulation study of the effects of cutter runout on milling process geometry is conducted using the models. It was found that the change of cutter radius for a tooth relative to its preceding one is the most important factor in evaluating the effects of cutter runout.