An apparatus for filling vials comprises a shelving unit defining an array of storage locations. The shelving unit may be an array in an XY plane or one or more carousels. A plurality of storage containers are provided, each removably carried by one of the storage locations. A counting and dispensing unit, a source of vials, a label printer and application unit or units, and an output device are also provided. The output device may take a variety of forms such as an output chute, which is preferably used when a capping unit is provided, an output conveyor, a plurality of output lanes, and an output carousel, which may be a dedicated carousel or a portion of the carousel providing the plurality of storage locations. A computer controlled engagement device provides motion in a Z direction. The engagement device may be comprised of a first stage for engaging the storage containers and a second stage for engaging the vials. A computer controlled system carries the engagement device and moves the engagement device in XY directions among the plurality of storage locations, counting and dispensing unit, source of vials, label printer and application unit, and output device. Methods of operating and refilling the vial filling apparatus are also disclosed.