The distribution of fluoride ions has been studied in the pure silica IFR, ITH, IWR, STF and STT zeolite structures using computational techniques. The interactions between the F- and SDA(+) ions (where SDA is the organic structure directing agent) are able to explain the F-cage occupation found experimentally. While studying the short-range fluoride-framework interactions, a relationship was found between the Si atoms forming the pentacoordinated units and the lowest F- defect energies, which rationalizes the experimental Si-F bonding in terms of energetic stability. It is proposed that the F- location is governed by a two step process. In a first stage, the electrostatic long-range forces and, especially, the interactions between the F- and the SDA(+) ions, decide which cage will be filled with F-; in a second stage, once the F- cage location is decided, the F- forms a covalent bond with a Si site to form an energetically stable pentacoordinated unit [SiO4/2F](-).