In certain segments of human DNA, the methylation of deoxycytidine res
idues has been found to be highly specific and interindividually conse
rved. Imprinted DNA sequences in diploid primary cells show allele-spe
cific differences in DNA methylation, usually with the active chromoso
mal regions being unmethylated and the inactive regions being methylat
ed. We show here that DNA from spermatozoa exhibits variations in alle
lic methylation patterns. Since germ cells are haploid, individual spe
rmatozoa can differ in DNA methylation patterns not only in the matern
ally or paternally derived allele, but also within each allele.