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In order to assess the feasibility of microsatellite primers as markers for genomic instability, we conducted a study of DNA stability in cauliflower callus. A protocol is described for the rapid screening of a large number of putative variant calli and plants. Genomic DNA is isolated and screened by microsatellite primers. We believe that inter-simple sequence repeat PCRs can conveniently detect and measure common genetic events underlying plant genomic instability. These include deletions, amplifications, translocations, insertions, recombination or chemical alterations. Our results indicate that instability occurred in an early step in the process of callogenesis. The technique is fast, reproducible, and is a new application for ISSR markers.