In this work five different imidazolium based ionic liquids, namely: 1-(2-oxybutyl)-3-methylimidazolium chloride, [C2OC2mIm][Cl]; 1-(2-oxypropyl)-3-methylimidazolium chloride, [C1OC2mIm][Cl]; 1-(3-hydroxypropyl)-3-ethylimidazolium chloride, [OHC3eIm][Cl]; 1-(3-hydroxypropyl)-3-methylimidazolium chloride, [OHC3mIm][Cl]; 1-(2-hydroxyethyl)-3-methylimidazolium chloride, [OHC2mIm][Cl], together with commercial 1-butyl-3-methylimidazolium chloride, [bmim][Cl] and synthesized protic imidazolium chloride, [Im][Cl], were prepared and their toxicity examined towards wheat and barley germination and growth. Introduction of the polar groups (in the form of hydroxyde and/or ether group) in the alkyl side chain of the imidazolium cation and their influence on the reduction of the ionic liquid's toxicity is demonstrated. The results indicate that toxicity of oxygen functionalized ILs is significantly lower against wheat comparing to non-functionalized analogues. In the case of barley, influence on germination follow the same trend as in the case of wheat, but for seedlings growth different trend is observed with more pronounced toxicity of ether functionalized ILs. From these results it was also shown that alkylation in the position N-3 atom of the imidazole significantly reduces toxicity of cation.