The role of structure directing agents in the synthesis of zeolites has been studied through atomistic simulation techniques. Three different kinds of structure directing agents have been reviewed: (i) isomorphic heteroatom Si --> Al and Si --> Ge substitutions; (ii) F(-) anions; and (iii) organic SDAs. The interplay between these structure directing agents is described and the separate effects of each one have been found from energy calculations and analysis of energetic terms.