The aim of this paper is to present a method of signal processing necessary for motion analysis in the trotting horse. Motion analysis is widely used to assess lameness in horses. By definition, lameness in trot is present if the movements during the stance phases of both fore or hind limbs differ. The motion of the horse is recorded using a system for motion analysis (Selcom, 1983, SELSPOT II User Manual, Pad Nr. 6710) and the vertical motion of the head during both stance phases is compared. The symmetry is analyzed comparing the values of the Fourier coefficients. Additional head movements are "single events" and present a problem. In this article we propose a mode of data processing using a system matched filter that neglects the nonperiodic additional movements and allows calculation of the representative Fourier coefficients. In comparison with a filtering method previously used in motion analysis this method is proved to be advantageous, as the precision of symmetry comparison increases.