Ploidy analysis can be performed by flow cytometry rapidly, accurately and with high precision. Since a flow cytometer can analyze hundreds or even thousands of individual nuclei per second, It can quickly screen hundreds of samples per hour and automatically determine the ploidy for each sample. The preparation of samples includes (1) extraction of the nuclei from cellular material, (2) staining of the nuclei with DAPI or another DNA stain, and (3) passing the nuclei through a mesh filter to remove cellular debris. The nuclei are then injected into the ploidy analyzer for analysis.