This paper introduces a formation method for 3-dimensional 6 ch.×6 ch. shuffling structures with graded-index (GI) circular core in a multimode polymer optical waveguide for optical printed circuit boards (OPCBs) using a unique photomask-free fabrication technique named the Mosquito method. The interchannel pitch of the fabricated waveguides is 250µm, where all the channels consist of both horizontal and vertical bending structures and the last 6 channels in parallel cross over the first 6 channels. We also report 3-dimensional S-shaped polymer waveguides. In the S-shaped waveguides, the first and last 6 channels with both horizontal and vertical core bending composing the above 3-dimensional shuffling waveguide are separated, in order to evaluate the effect of over-crossing on the loss. It is experimentally confirmed that there is no excess insertion loss due to the shuffling structure in the 3-D shuffling waveguide. The evaluated crosstalk of the 3-D shuffling waveguide is lower than -30dB. The 3-D shuffling waveguide proposed in this paper will be a promising component to achieve high bandwidth density wiring for on-board optical interconnects.