Abstract: A solid phase synthesis system including one or more reaction vessels, one or more structural unit chemical dispensing units, one or more synthesis chemical dispensing units, and a controller is provided. The arrangement of the reaction vessels, dispensing units and corresponding fluid interconnections restricts cross-contamination within the system. The controller facilitates automated or semi-automated production of various organic compounds. Associated software including varying command structures may be provided to facilitate ease in programming and automating of the synthesis system.