Water immiscible ionic liquid 1-dodecyl-3-methylimidazolium tetrafluoroborate (DMIM-BF4) and its inclusion complex with beta-cyclodextrin (beta-CD) in molar ratio 1:1 have been synthesized. The formation of DMIM-BF4/beta-CD complex was confirmed by FT-IR analysis, H-1 NMR analysis, and differential scanning calorimetry data. Our results indicate that the aliphatic tail of DMIM-BF4 is included into beta-CD inner cavity whereas imidazolium ring is located outside the torus. Moreover, the weak interaction between polar components of ionic liquid and hydrophilic outer surface of beta-CD has also been detected. The standard agar disk diffusion method was performed to evaluate antimicrobial efficiency of the obtained compounds against Staphylococcus aureus (ATCC-25923), Escherichia coli (ATCC-25922) and Pseudomonas aeruginosa (ATCC-27853), Candida albicans (M 885 ATCC 10231) and its clinical isolate test-cultures. It has been found that both DMIM-BF4 and DMIM-BF4/beta-CD complex possess high antimicrobial activity as revealed by similar zone inhibition values against all tested microorganisms. The acute toxicity studies on Danio rerio (zebrafish) model organism showed that the pure ionic liquid DMIM-BF4 is slightly toxic compound having LD50 value of 7 mg/L, whereas DMIM-BF4/beta-CD complex has considerably reduced toxicity (LD50 = 100 mg/L) and therefore have potentially wider application areas. (C) 2015 Elsevier B.V. All rights reserved.