A highly sensitive biosensor based on a silicon photonic crystal waveguide incorporating microcavities is investigated using two-dimensional Finite Difference Time Domain method. With a microcavity placed near the waveguide, a dip is observed on the waveguide transmission spectrum, corresponding to the resonance wavelength of the cavity. Any change of the medium surrounding to the waveguide and cavity results in the shift of the dip in the transmission spectrum. Our simulation shows an optimal geometry of the cavity nearby the waveguide to have high sensitivity. Several materials with refractive indices ranging from 1 (the air) to 1.57 (Bovine serum albumin - BSA) were studied and showed that the best sensitivity of 194 nm/RIU and limit of detection of 5×10-5 RIU can be achieved. The varied resonance wavelength as a second-order polynomial function of refractive index was observed. The sensor is appropriate for detecting homogeneous medium.