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A polarization-insensitive interleaver using a multilayer waveguide structure is proposed. The device consists of two core guiding layers separated by a cladding layer. A Mach-Zehnder interferometer-based (MZI) interleaver was fabricated at the lower layer, whereas a channel waveguide was fabricated at the top layer just over one arm of the MZI. In this design, the required transverse-electric (TE) and transverse-magnetic (TM) optical signal paths to conduct a polarization-insensitive MZI-based interleaver could be easily achieved through two vertically coupled polarization splitters. The device exhibited complete polarization insensitivities with respect to the center wavelength and channel spacing over the entire C-band. The channel isolation, insertion loss, and polarization-dependent loss of the device were 18, 8.8, and 0.8 dB, respectively.