An apparatus for filling pharmaceutical containers includes a filling device with a linear transport device that preferably includes circulating holding elements for the containers. The holding elements are movable along a transport direction from a coupling side to a decoupling side of the transport device. A processing station includes a filling station arranged at the transport device for filling the containers with a pharmaceutical substance. A coupling element transfers the containers to the transport device, and a decoupling element receives the containers from the transport device. A first feed unit provides containers of a first type to be filled, and a second feed unit feeds containers of a second type to be filled. An interface element is arrangeable on the feed side with respect to the transport device. Containers of the first type or the second type can be selectively fed directly or indirectly to the transport device.