Molecules that only differ by their chirality, so called enantiomers, often possess different properties with respect to their biological function. Therefore, the separation of enantiomers presents a prominent challenge in molecular biology and belongs to the ``Holy Grail'' of organic chemistry. We suggest a new separation technique for chiral molecules that is based on the transport properties in a microfluidic flow with spatially variable vorticity. Because of their size the thermal fluctuating motion of the molecules must be taken into account. These fluctuations play a decisive role in the proposed separation mechanism.