To capture the characteristics and changes in barley endosperm tissue at different stages of seed development at the molecular level, a custom Agilent microarray representing 42,847 barley sequences (selected from a total of 50,938 unigenes from HarvEST assembly 35) was used for global gene expression profiling at 12 time points between 0 and 20 days after pollination. By hierarchical clustering and principal component analysis, trends of gradual transition in gene expression were observed, indicating global relationships between developmental stages. Analysis of Variance was then used to identify the differentially expressed genes between adjacent time points. Gene ontology (GO) enrichment analysis then highlighted that among the significantly changed genes, categories of biological processes, cellular components and molecular functions related to the seed development were highly enriched. A gene co-expression network was constructed using all the significantly differentially expressed mRNAs, resulting in the discovery of functional modules of genes and biological processes. We then investigated specific classes of genes (e.g. cell wall related) in more detail within the overall context of the derived network. The results of these analyses will be presented and discussed.