Calcium-dependent protein kinases (CDPKs) are important sensors of Ca(+2) flux in plants, which control plant development and responses by regulating downstream components of calcium signaling pathways. Availability of the whole genome sequence and microarray platform allows investigation of genome-wide organization and expression profile of CDPK genes in rice with a view to ultimately define their function in plant systems. Genome-wide analysis led to identification of 31 CDPK genes in rice after a thorough annotation exercise based upon HMM profiles. Twenty-nine already identified CDPK genes were verified and two new members were added to the CDPK gene family of rice. Relative expression of all these genes has been analyzed by using Affymetrix rice genome arraytrade mark during three vegetative stages, six stages of panicle (P1-P6) and five stages of seed (S1-S5) development along with three abiotic stress conditions, viz. cold, salt and desiccation, given to seedling. Thirty-one CDPK genes were found to express in at least one of the experimental stages studied. Of these, transcripts for twenty three genes accumulated differentially during reproductive developmental stages; nine of them were preferentially up-regulated only in panicle, five were up-regulated in stages of panicles as well as seed development, whereas, expression of one gene was found to be specific to the S1 stage of seed development. Eight genes were found to be down-regulated during the panicle and seed developmental stages. Six CDPK genes were found to be induced while the expression of one gene was down-regulated under stress conditions. The differential expression of CDPK genes during reproductive development and stress is suggestive of their involvement in the underlying signal transduction pathways. Furthermore, up-regulation of common genes both during reproductive development as well as stress responses is indicative of common element between reproduction and stress.