Disadvantages
As mentioned above, the CCE separates cells based on their sedimentation property but not specific features (e.g. surface protein, cell shape). It cannot separate different types of cells which have similar sedimentation properties. This means that previous purification needs to be done for mixed cell type sample. The CCE is also limited to cells which are able to be individually suspended in the buffer solution. Cells which always attach to something cannot be separated by the CCE.
Read more about this topic: Counterflow Centrifugation Elutriation