3D photonic crystals (PhCs) and photonic bandgap (PBG) materials have attracted considerable scientific and technological interest. In order to provide functionality to PhCs, the introduction of controlled defects is necessary, the importance of defects in PhCs is comparable to that of dopants in semiconductors. Over the past few years, significant advances have been achieved through a diverse set of fabrication techniques. While for some routes to 3D PhCs, such as conventional lithography, the incorporation of defects is relatively straightforward; other methods, for example, self-assembly of colloidal crystals (CCs) or holography, require new external methods for defect incorporation. In this review, we will cover the state of the art in the design and fabrication of defects within 3D PhCs. The figure displays a fluorescence laser scanning confocal microscopy image of a y-splitter defect formed through two-photon polymerization within a CC.