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This paper demonstrates that polarization plays an important role in the formation of interference patterns, pattern contrasts, and periods in four-beam interference lithography. Three different polarization modes are presented to study the effects of polarization on four-beam laser interference based on theoretical analysis, simulations, and experiments. A four-beam laser interference system was set up to modify the silicon surface. It was found that the secondary periodicity or modulation was the result of the misaligned or unequal incident angles only in the case of the TE-TE-TM-TM mode. The resulting patterns have shown a good correspondence with the theoretical analysis and simulations.