The origin of the low transmission through the low energy beam line between the electron cyclotron resonance source and the AGOR cyclotron has been investigated. Measurements of beam size and emittance, determined with the “varying quadrupole method,” are compared with calculations including fringe fields up to third order with the code COSY INFINITY. Calculations and measurements qualitatively agree; the calculations exhibit the large beam losses observed. On the basis of the calculations new settings have been determined, resulting in a significant increase of the transmission. To achieve full transmission a complete redesign of the beam line, in particular of the bending magnets, is needed.