Three-dimensional (3D) photonic crystals can block photons in any direction and are expected to make possible their ultimate control. However, creating 3D crystals without any unintentional defects over large areas at optical wavelengths has been challenging. For example, opal-based crystals inevitably contain unintentional defects, it is difficult to increase the sizes of micro-manipulated crystals over approximately 6 microm and producing stacked 3D crystals with thin 2D layers requires complicated and time-consuming processes. So far, these difficulties have hindered 3D photonic-crystal research. Here, we demonstrate a novel top-down approach to creating 3D crystals that overcomes these difficulties and significantly simplifies the process. We have developed a double-angled deep-etching method, which enables the direct creation of 3D woodpile crystals in single-crystalline silicon. A strong photonic bandgap effect with >20 dB attenuation in all directions has been achieved. Furthermore, bonding a light emitter onto or between 3D crystals created in this way has been shown to enhance or suppress spontaneous emission.