MCPA (4-chloro-2-methylphenoxy) acetic acid is a common synthetic auxin used as a herbicide. The purpose of this study was to determine the effects of four new forms of MCPA being the herbicidal ionic liquids (HILs) with MCPA as an anion and two previously known formulations (potassium–sodium salt and 2-ethylhexyl ester) on seed germination and seedling development of winter oilseed rape (Brassica napus). Rape plants are susceptible to MCPA and volunteers can be a big problem in crop rotation. Seedling fresh weight and root length were quantified, mitotic activity, as well as lipid, starch, hydrogen peroxide and polyphenol contents were assessed by light and fluorescence microscopy and the computer-aided cytophotometer. In primary roots mitotic activity was almost completely inhibited under the influence of herbicides, cell elongation zones and root hair zones were significantly reduced, and a characteristic bolded root segment formed just above a meristem. In contrast to the traditional salt formulation the new HILs were weak inducers of hydrogen peroxide synthesis, but were potent stimulators of the synthesis of phenolic compounds and storage as well as emergency substances such as lipids and starch. All tested forms of MCPA caused strong phytotoxic effect on winter rape seedlings, but the tested HILs were more effective.