This thesis is focused on the synthesis and application of ionic liquids in organic synthesis. A library of novel imidazolium ionic liquids was designed and synthesised in efforts to find molecules which had reduced anti-microbial toxicity and increased aerobic biodegradation. Synthesis of novel ionic liquids has been carried with efficient and easy methods to achieve atom economy, reduced number of steps and high yields. Ionic liquids synthesized in the lab have been tested either as a catalyst in acetalization reactions, or as a solvent in Carbonyl-Ene reactions. These studies have given excellent results and clearly demonstrated the potential and applicability of ionic liquids in organic synthesis. Working with our collaborators, anti-microbial toxicity and biodegradation of these ionic liquids has been studied. Preliminary studies of the toxicity of all ionic liquids were performed against a panel of 12 fungi and 8 bacterial strains. Antifungal and antibacterial toxicity studies demonstrated that most of these ionic liquids did not inhibit the growth of any organism screened at concentrations of 2.0 mM. Biodegradation studies of the novel of novel ionic liquids have also been performed and have given valuable information on the next step in rational design towards novel readily biodegradable ionic liquids.