Ionic liquids (ILs) are liquids composed entirely of ions, therefore they screen every charged perturbation and present ionic conductivity. Recent studies focus in particular on the so-called room temperature ionic liquids (RTILs), that are organic/inorganic salts with melting point or glass transition below 100 C, whose chemical-physics properties are greatly affected by their ionic character. The dissociation of molecules into ions gives origin to an interplay between multiple interactions such as Coulomb forces, dispersion forces and hydrogen bonding (HB). The latter is crucial for the structural organisation of the liquids, which furthermore is intertwined with proton conduction, a key feature for applications in electrochemical energy conversion devices. In this thesis we show how HB influences the structure, dynamics and proton conduction of prototypical ILs.