The present invention provides an automated system and method for packing chromatography columns. In one embodiment, the system first determines the type of media that is present in the column, and uses this information to generate an automated procedure to pack the specific media type. In a second embodiment, the media type is made known to the system, such as via input from the operator. The system then uses this information, in the same manner as in the first embodiment, to generate an automated procedure to pack the specific media type. Finally, in a third embodiment, parameters such as column height and rate of compression are made known to the system, such as via input from the operator. The system then packs the column in accordance with these supplied parameters.