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Photonic crystals (PCs) are a promising technology for the realization of high-density optical integrated circuits. PC-based couplers have been proposed as a compact means of achieving wavelength multiplexing and demultiplexing. However, the performance of such devices can be limited by fabrication imperfections such as rod size nonuniformities. In this paper, coupled mode theory (CMT) is applied in order to study the implication of the variation of the size of the rods. CMT can provide a useful insight in the effect of size variations, and unlike other numerical methods such as the finite difference time domain, it does not require excessive computational time. Using CMT, the relation between the size nonuniformities and the coupler's insertion loss and extinction ratio is analyzed. It is shown that even a small size variation of the order of 2%-3% can degrade the performance of the device.