The effect of fluorine substitution on a series of hydrogen-bonded (HB) systems has been studied with the aid of theoretical ab initio methods. The effect on HB donors has been examined using a series of fluoromethane derivatives as hydrogen bond donors in their interaction with water. The results indicate a 0.1 Å shortening of the HB bond distance for each additional fluorine atom and 1 kcal/mol increase for the interaction energy. The fluorine effects have been considered in several HB acceptors like hexafluorobenzene and a series of small molecules. The π-cloud of hexafluorobenzene forms stable complexes with electron rich atoms, behaviour that is the opposite to what is observed for benzene. For the small molecules acting as HB acceptors, a weakening of the HB is observed. In some cases, the effect is so important that HB properties are reverted as the case of the hexafluorobenzene. Finally, the atomic properties of a series of charge transfer and HB complexes have been compared.