Developing seeds consist of genetically distinct maternal and filial tissues, whose interactions during development are largely unknown. To better understand the molecular physiology of developing seed tissues in barley, we created a high-density cDNA macroarray bearing 711 cDNA fragments from 691 clones representing at least 620 unique genes mainly derived from a cDNA library constructed with mRNA from the early stages of caryopsis development. This array has been used to compare gene expression patterns in maternal pericarp and filial embryo sac tissues of caryopses sampled 1-7 days after flowering (DAF). The profiles obtained for both tissues revealed that at least 26 genes in pericarp and 12 genes in embryo sac tissues were up-regulated by more than a factor of two during this period. RNAs expressed at high levels in the pericarp mainly encode enzymes involved in carbohydrate and lipid metabolism, but also include mRNA for a transcription factor related to FILAMENTOUS FLOWER (FIL). Genes preferentially expressed in the embryo sac are mainly related to degradation and/or processing of proteins or are involved in the process of starch accumulation, which begins in the seed at this time. Some of the most conspicuously regulated genes were studied in more detail by Northern analysis and in situ hybridization. The mRNA with the highest apparent signal intensity encodes a methionine synthase (MSY). MSY is highly expressed throughout the pericarp and to a lower extent in the transfer cell layer of the endosperm. Of special interest is a gene of unknown function because its high-level expression is restricted to the nucellar projection, the maternal transfer tissue of the caryopsis. This gene, represented by clone HY09L21, may play a central role in transport processes and thus in embryo growth.