Twelve piperazinium- and guanidinium-based ionic liquids (ILs) were synthesized, and characterized by (1)H nuclear magnetic resonance (NMR), thermal gravimetric analyzer (TGA) and differential scanning calorimetry (DSC). The antimicrobial activity and cytotoxicity have been investigated to provide the information whether the newly synthesized ILs are toxic or not. The antimicrobial effects of these ILs on gram negative and gram positive bacteria are evaluated on the basis of the minimum inhibitory concentration (MIC) measurements. The membrane damages of bacteria in the presence of ILs are observed by scanning electron microscopy (SEM). The cytotoxicity data of the ILs on HEK-293 and C6 cells are obtained by MTT cell viability assay. The disruption of cell cycle is analyzed by the flow cytometry. The results show that most of the ILs exhibit low toxicity, and the ILs with tetrafluoroborate anion and with benzene ring on cation are the species with relatively high toxicity among the studied ILs. The fundamental data and results can provide some useful information for the further studies and applications of the ILs.