As the first attempt, ionic liquid solutions have been employed for direct extraction of proteins from yeast cells. Compared with effects of 21 different ionic liquid solutions on the extraction efficiency, 3-(dimethylamino)-1-propylaminium formate ([DMAPA]FA) was selected as the suitable ionic liquid solution. As this ionic liquid can be easily removed under vacuum, contamination by the chemical noise can be effectively reduced. Both sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and 2-dimensional gel electrophoresis (2-DE) were employed to separate numerous proteins, and the results indicated that the chemical properties of target proteins remained unchanged during the extraction process. Furthermore, extracted proteins were applicable to the standard method for Western blotting which showed proteins maintain immunoreactivity and biological functions. These investigations indicated that the ionic liquid [DMAPA]FA is a promising reagent for protein extraction in yeast cells.