The three-dimensional (3D) interconnection of waveguides in planar lightwave circuits (PLCs) is demonstrated. A femtosecond laser successfully interconnects the waveguides of PLCs with low loss by writing 3D waveguides in the PLCs. A directly written waveguide with a length of about 2000 µm crossed over another waveguide without any interaction. The excess losses at 1550 nm were 2.7 and 2.8 dB for the transverse electric (TE) and transverse magnetic (TM) modes, respectively.