Epigenetic variation describes heritable differences that are not attributable to changes inDNA sequence. Methylation of cytosine residues provides a mechanism for the inheritance of epigenetic information. Genome-wide methylation patterns of the maize inbreds B73 and Mo17 were compared using methylated DNA immunoprecipitation followed by hybridization to custom designed microarrays (meDIP-chip). DNA methylation levels are higher near the centromeres and are generally inversely correlated with recombination and gene expression levels. A comparison of the DNA methylation levels between inbred genotypes identified ~700 differentially methylated regions. The regions of differential methylation between inbredsoften occur in intergenic regions but some of these regions are located within or near genes.There is evidence that variation in DNA methylation levels can occur in genomic regions that are identical-by-descent, illustrating the potential for epigenetic variation that is not tightly linked to genetic changes. The many detected examples of epigenetic variation provide a glimpse of the epigenetic variability, uniformity, and inheritance in maize.