Growth on deeply patterned substrates, i.e. on pillars instead of a continuous substrate, is expected to be very promising to get crack free epilayers on wafers without any bowing. We report here on a structural investigation of GaAs MBE deposited on patterned (001) ocut Si, consisting of pillars 8 µm high and 5 to 9 µm wide, to check mostly the behaviour of the threading dislocations. It is found that only very rarely they propagate up to the GaAs top that will serve as active region in devices. Twins were also detected which sometimes reached the topmost part of GaAs. However, as twins have no associated dangling bonds, they should not be electrically active. Rare antiphase boundaries exist at the interface, hence not harmful for device operation.