We investigated the methylation state of a set of storage protein genes of maize, coding for zeins and glutelins, in different somatic tissues and in developing endosperms. These genes, present as multigene families in the maize genome and organized in clusters on different chromosomes, are coordinately and specifically transcribed only in endosperm cells. Southern blot analysis of DNA digested with methylation-sensitive restriction enzymes shows a specific and extensive undermethylation of zein and glutelin sequences in the endosperm, while a common methylated pattern is detected in the different somatic tissues and in the embryo. However, a constant fraction of endosperm DNA (∼35%) is methylated at all zein sequences, which are found to be heavily modified in pollen DNA as well. Undermethylation is extended along a zein cluster and cannot be explained by reduced levels of 5-methylcytosine in endosperm DNA with respect to other tissues. The undermethylated state of storage protein genes is already established at an early stage of endosperm development, when transcripts levels for both genes are almost undetectable.