In order to obtain detailed information about the genes expressed at the initial stages of rice (Oryza sativa) seed development, we investigated gene expression profiles in the wild type and endospermless (enl) mutant, at 2–3 days after pollination (DAP) and at 4–6 DAP by microarray analysis. Using rice 22k custom oligo DNA microarray, the intensity of gene expression in the wild type seeds at 2–3 DAP (WT-3D) was compared with that in other groups. As a result, 1,620 clones (22k spots on the array glass) exhibited differential hybridization signals. Although homology searches were conducted for these clones, the function of half of them remained unknown. Based on the comparative analysis of the gene expression profile in the wild type and enl mutant, the following results were obtained. The intensity of expression of about 1,000 genes changed from the 2–3 DAP to the 4–6 DAP stages. At the earliest stage (2–3 DAP), genes for defense against diseases or response to stressagents as well as genes for transporter proteins were strongly expressed. At the succeeding stage (4–6 DAP), genes for storage proteins, genes for enzymes of starch synthesis and genes for a transcription factor (zinc finger) were strongly expressed. These results suggest that microarray analysis is useful to elucidate the molecular mechanisms of endosperm formation through the characterization of the genes expressed at each stage of seed development. Despite a change in the expression of gene intensity at both stages of development, gene functions could not be identified. Extensive investigations should be carried out to reach a definitive conclusion.