Little reliable information exists about the genetic events that control the onset and timing of seed-fill in soybean cotyledons. To identify the genes involved in this process, cDNA libraries were prepared from mRNAs isolated from seeds at 7 and 21 days after flowering (DAF), which represent times just before and after the initiation of seed-fill. For the soybean variety Resnik, which was used for this study, seed-fill and the establishment of an endoreduplicative cell cycle occurred 12–14 DAF. Suppression subtractive hybridization was then applied to identify sequences that were differentially expressed at each of these two developmental stages. False positives in the libraries were reduced by using mirror orientation selection (MOS). The libraries of differentially expressed genes that resulted were analysed and the nucleotide sequences obtained were compared with those in existing databases. Several genes from each library were chosen and their expression profile during seed development was analysed by quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) using RNA preparations originating from different seed developmental stages. Candidate genes for control of the stage shift from dividing cells to endoreduplication were identified.