About 1% of the mouse genome is cleaved by Hpa II to give a discrete fraction on gels. The nonmethylated fraction is present in all tested tissues, including sperm, and contains Hpa II sites at about 15 times their frequency in bulk DNA. About 80% of the fraction is composed of sequences that occur once or a few times per genome; the remainder is largely rDNA. Unlike bulk DNA, the fraction is not deficient in CpG, and this may be directly due to the lack of methylation. Genomic mapping of three nonribosomal fragments showed that they are part of islands of DNA within which nonmethylated Hpa II and Hha I sites are highly concentrated. We estimate about 30,000 islands per haploid genome and discuss evidence that many may be associated with genes.