We present a space-domain integral-equation method for the analysis of periodic structures formed by three-dimensional metallic objects arranged in a general skewed two-dimensional lattice. The computation of the space-domain Green's function is accelerated using the Ewald transformation. The method is validated on several periodic structures ranging from planar frequency-selective surfaces to three-dimensional photonic crystals and metamaterials. For these structures, our technique shows a clear advantage in terms of computational speed when compared with available commercial softwares.