The influence of the two most commonly used ionic liquids (1-butyl-3-methyl imidazolium tetrafluoroborate, [BMIM][BF4], 1-butyl-3-methyl imidazolium hexafluorophosphate, [BMIM][PF6]) and three selected organic solvents (dimethylsulfoxide, ethanol, methanol) on the growth of Escherichia coli, Pichia pastoris and Bacillus cereus was investigated. [BMIM][BF4] was toxic at 1% (v/v) on all three microorganisms. The minimal inhibitory concentration (MIC) of [BMIM][BF4] on E. coli growth was between 0.7 and 1% (v/v). In contrast, [BMIM][PF6] was less toxic for P. pastoris and B. cereus, whereas E. coli was not able to tolerate [BMIM][PF6] (MIC value: 0.3-0.7% v/v). Growth of P. pastoris was unaffected by [BMIM][PF6] at 10% (v/v). Similar results were found for dimethylsulfoxide. Thus, ionic liquids (ILs) can have substantial inhibitory effects on the growth of microorganisms, which should be taken into account for environmental reasons as well as for the use of ILs as co-solvents in biotransformations.