We report on the fabrication and testing of Si-based photonic crystal waveguides for use and integration with microfluidic and cell-based bioanalytical devices. Single-row, defect-mode waveguides were placed atop steep isolation ridges that provide in-plane and out-of-plane optical access, as well as deep channels that are well-suited for biofluid transport and interface to cellular and molecular systems. A 20 dB attenuation in optical transmission at 1540 nm was measured, confirming the existence of a near-IR optical bandgap.