Rice enters its most chilling-sensitive stage at the onset of microspore release. The microsporocytes produce a wall of callose between the primary cell wall and the plasma membrane, and it has been shown that precise regulation of callose synthesis and degradation in the anther is essential for fertile pollen formation. A cDNA for β-1,3-glucanase was isolated from rice anther and named Osg1. RT-PCR analysis revealed that Osg1 transcripts were present in leaves, roots, and anthers. Genes for 10 callose synthases in the rice genome were fully annotated and phylogenetically analyzed. Expression analysis of these genes showed that OsGSL5, an ortholog of microsporogenesis-related Arabidopsis AtGSL2, was specifically expressed in anthers, and was notably downregulated by chilling treatment. Rho-type small GTP-binding proteins are molecular switches that control callose synthase activity. Their gene expression profiles in rice anther were also analyzed. The gene expression profile during the microspore development process under chilling stress was revealed using cDNA microarray. Three novel genes whose expression levels were remarkably changed by chilling in rice anther were identified. A new cis element that includes a DNA transposon Castaway sequence was found in the 5' upstream region of two genes which were conspicuously down-regulated by chilling temperatures in rice anther. Analyses of these chilling-responsive genes are not only fundamental to the understanding of mechanisms that underlie chilling injury in rice pollen, but are also essential to the creation of a chilling-tolerant rice plant.