We have synthesized and determined the electrochemical and thermal stabilities of a series of 1-methyl-3-alkoxyalkyl and 1-methyl-3-fluoroalkyl imidazolium and the corresponding pyrrolidinium-based ionic liquids and estimated the cytotoxicities of representative ionic liquids. The pyrrolidinium-TFSI based ionic liquids have wide electrochemical stability (>5.7–6.2V vs. Li/Li+) but show limited thermal stabilities and lithium cell discharge characteristics, as compared to those that are imidazolium-based (4.8–5.1V vs. Li/Li+). The fluoroalkyl-derived ionic liquids typically have superior thermal stability (T d >350°C) as compared to the alkoxyalkyl-substituted analogues. In all these cases, TFSI− anion-based ionic liquids are thermally and electrochemically more stable than the BF4 − anion-based analogues. We have also shown that the imidazolium-based ionic liquids are relatively nontoxic and their EC50 values are comparable to their corresponding lithium salts.