A dual paddle end effector robot is disclosed which is capable of parallel processing of workpieces. The end effector includes a lower paddle rotatably coupled to an end of the distal link, and an upper paddle rotatably coupled to the lower paddle. The lower paddle supports a drive assembly capable of rotating the upper paddle with respect to the lower paddle. In one embodiment of the present invention, the dual paddle end effector robot may be used within a wafer sorter to perform parallel processing of workpieces on a pair of aligners within the sorter. In such an embodiment, the robot may first acquire a pair of workpieces from adjacent shelves within the workpiece cassette. After withdrawing from the cassette, the respective paddles on the end effector may fan out and transfer the wafers to the chucks of the respective aligners. After processing of the workpieces on the aligners is complete, the fanned end effector paddles may re acquire the workpieces, the upper paddle may return to its home position located directly over the lower paddle, and then return the processed workpieces to their original cassette or to a new cassette. Parallel processing of workpieces in this fashion provides significantly greater throughput than in conventional wafer sorter systems. Throughput may be improved still further by providing buffering locations for the workpieces at the respective aligners.