In this talk the systematic errors of emittance measurements at the 250MeV Injector test stand for the SwissFEL are discussed. Errors in the determination of the beam size and inaccuracies in the knowledge of the transfer matrices, mainly induced by beam energy uncertainties, are analysed using Monte-Carlo-Techniques. The effect of deviations from a perfect matched optics in the diagnostic FODO lattice is an important contribution to the relevant systematic errors.