An automated small particle distribution system is provided for transferring small particles from source tubes to destination tubes. The system includes a loading deck that is structured and operable to store and provide a plurality of source tube trays and a plurality of destination tube trays. Each source tube tray includes a plurality of source tubes stored therein, and each destination tube tray includes a plurality of destination tubes stored therein. The system additionally includes a work deck is structured and operable to receive selected source tube trays and selected destination tube trays from the loading deck, aspirate various specified amounts of small objects stored in selected source tubes, and deposit the aspirated small objects into selected destination tubes without cross-contamination of small objects.