The present invention provides apparatus and methods for the synthesis of combinatorial chemical libraries. The apparatus comprises a plurality of reaction vessels having an inner surface, an outer surface, a first opening, and a second opening. An agitator is contained within each of the reaction vessels for stimulating liquid circulation within the vessels. The apparatus has a common gas line having a plurality of gas outlet ports, where each of the reaction vessels has at least one gas outlet port positioned to feed into the vessel. The apparatus also has a common liquid line having a plurality of liquid outlet ports, where each of the reaction vessels has at least one liquid outlet port positioned to feed into the vessel. Each reaction vessel also has at least one valve coupled to the second opening on the vessel.