A microorganism screening system includes a container configured to store a liquid containing microorganism particles and a liquid medium, and a microorganism separation device. The microorganism separation device includes a hydrodynamic separation device and a liquid feeding unit configured to supply the liquid from the container to the hydrodynamic separation device. The hydrodynamic separation device includes a curved flow channel having a rectangular cross-section, and is configured to separate the liquid into a first segment containing relatively large microorganism particles and a second segment containing relatively small microorganism particles through use of a vortex flow generated in the liquid flowing through the curved flow channel. Screening for microorganisms can be performed efficiently.