SummaryA procedure is described to isolate DNA probes from the bovine genome that are enriched in sites for the so‐called rare cutter restriction endo‐nucleases. A collection of SacII (CvCGCGG)‐Hin‐dlll fragments from bovine sperm was established in the plasmid Bluescript. 180 clones were picked at random and analysed for the presence of inserts with sites for the following rare cutters:EagI,BsshII,NarI,MluI,NruI,NaeI: 70% of the clones contained at least 1 site and 5% contained four different such sites. 22.8% had multiple sites for one or more of the rare cutters tested. Sequence analysis for 16 clones confirmed the cloning of DNA with a G+C content and a proportion of CpGvsGpCs indicative of CpG