The magnetotransport properties of antidot lattices containing artificially designed grain boundaries have been measured. We find that the grain boundaries broaden the commensurability resonances and displace them anisotropically. These phenomena are unexpectedly weak but differ characteristically from isotropic, Gaussian disorder in the antidot positions. The observations are interpreted in terms of semiclassical trajectories which tend to localize along the grain boundaries within certain magnetic field intervals. Furthermore, our results indicate how the transport through superlattices generated by self-organizing templates may get influenced by grain boundaries.