Reciprocal crosses between plants containing different genome numbers have been demonstrated to show alternate phenotypes in many species and are often lethal. The effects of interploidy crosses on kernel development in maize (Zea mays) have been reassessed using markers for two cell domains: the aleurone and the basal endosperm transfer layer (BETL); and by monitoring gene expression. The study confirms previous observations and offers novel insights into genomic interactions. Endosperms from maternal excess crosses (tetraploid mother, diploid father) displayed reduced mitotic activity, and an accelerated rate of differentiation generally, including early starch accumulation, and earlier, atypical aleurone formation. The BETL failed to form normally, being replaced with aleuronelike cells, except for a few interspersed cells. Gene expression was altered, including those encoding cell domain markers and storage molecules. Paternal excess endosperms (diploid mother, tetraploid father), showed an increase in cellular proliferation. Generally, differentiation was delayed: starch accumulation began late, and formation of the aleurone layer was delayed, and was morphologically highly irregular. BETL specification was also disturbed, with only a few cells showing characteristic wall modifications very late in development. Later development of the whole endosperm was characterized by ectopic gene expression, and zones of high cell proliferation. A greater proportion of the genome was mis-expressed in these crosses, reflecting the more extreme phenotype. Although expression levels of marker genes did not reflect the failure to develop a normal BETL, it may be that the cells in the BETL region had undergone an modified developmental program. This work is considered in the context of evolutionary models which state that different parental roles lead to differential expression of genes from their respective genomes, and is compared with evidence from arabidopsis. The current study is considered generally supportive of such models.