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In this paper, we present a rigorous coupled-wave analysis (RCWA) of absorption enhancement in all-silicon (Si) photodiodes with integrated hole arrays of different shapes and dimensions. The RCWA method is used to analyze the light propagation and trapping in the photodiodes on both Si-on-insulator (SOI) and bulk Si substrates for the datacom wavelength at about 850 nm. Our calculation and measurement results show that funnel-shaped holes with tapered sidewalls lead to low back-reflection. A beam of light undergoes a deflection subsequent to the diffraction in the hole array and generates laterally propagating waves. SOI substrates with oxide layers play an important role in reducing the transmission loss, especially for deflected light with higher-order diffraction from the hole array. Owing to laterally propagating modes and back-reflection on the SiO2 film, light is more confined in the thin Si layer on the SOI substrates compared to that on the bulk Si substrates. Experimental results based on fabricated devices support the predictions of the RCWA. Devices are designed with a 2-μm-thick intrinsic layer, which ensures ultrafast impulse response (full-width at half-maximum) of 30 ps. Measurements for integrated photodiodes with funnel-shaped holes indicate an enhanced external quantum efficiency of more than 55% on the SOI substrates. This represents more than 500% improvement compared to photodiodes without integrated phototrapping nanoholes.