An apparatus for microwave assisted solid phase synthesis using solid-phase resin beads mixed with a liquid solvent comprising a generally cylindrical reactor made of microwave transparent material and having a central axis, the reactor having an inlet and an outlet; a porous frit associated with the outlet of the reactor, the porous frit preventing discharge of beads and allowing discharge of the solvent from the reactor; and means for concentric rotation of the reactor around the central axis in alternating clockwise and anti-clockwise directions. A method for microwave assisted solid phase synthesis using the apparatus is also disclosed.