A review on silica clathrate compounds, which are variants of pure silica zeolites with relatively small voids, is presented. Zeolites have found many uses in industrial and domestic settings as materials for catalysis, separations, adsorption, ion exchange, drug delivery, and other applications. Zeolites with pure silica frameworks have attracted particular interest because of their high thermal stability, well-characterized framework structures, and simple chemical compositions. Recent advances in new synthetic routes have extended the structural diversity of pure silica zeolite frameworks. Thermochemical analyses and computational simulations have provided a basis for applications of these materials and the syntheses of new types of pure silica zeolites. High-pressure and high-temperature experiments have also revealed diverse responses of these framework structures to pressure, temperature, and various guest species. This paper summarizes the framework topologies, synthetic processes, energetics, physical properties, and some applications of silica clathrate compounds.