Photonic crystals1-3offer unprecedented opportunities for miniaturization and integration of optical devices. They also exhibit a variety of new physical phenomena, including suppression or enhancement of spontaneous emission, low-threshold lasing, and quantum information processing4. Various techniques for the fabrication of three-dimensional (3D) photonic crystals-such as silicon micromachining5, wafer fusion bonding6, holographic lithography7, self-assembly8,9, angled-etching10, micromanipulation11, glancing-angle deposition12and auto-cloning13,14-have been proposed and demonstrated with different levels of success. However, a critical step towards the fabrication of functional 3D devices, that is, the incorporation of microcavities or waveguides in a controllable way, has not been achieved at optical wavelengths. Here we present the fabrication of 3D photonic crystals that are particularly suited for optical device integration using a lithographic layer-by-layer approach15. Point-defect microcavities are introduced during the fabrication process and optical measurements show they have resonant signatures around telecommunications wavelengths (1.3-1.5 μm). Measurements of reflectance and transmittance at near-infrared are in good agreement with numerical simulations.