An apparatus and method for loading a plurality of substrates into a substrate holder in a loading chamber of a deposition reactor to form a vertical stack of horizontally oriented substrates within said substrate holder, for turning the substrate holder to form a horizontal stack of vertically oriented substrates, and for lowering the substrate holder into a reaction chamber of the deposition reactor for deposition. The technical effects achieved are: a top loading system for a vertical flow deposition reactor in which the substrates can be loaded with horizontal orientation, eliminating the need for flipping each substrate separately by flipping the whole substrate holder and minimizing a loading distance in a reactor cluster.