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Large-scale gene expression analyses were conducted during embryonic development of Capsella bursa-pastoris using the cDNA-AFLP technique, and 231 differentially expressed genes were identified. Most of the transcript-derived fragments (TDFs) were identified against Arabidopsis sequences and a minority against other plant sequences by searching in NCBI database. A total of 128 TDFs, homologous to genes with known functions, were classified into 13 functional categories, and many of them were involved in transcription, metabolism, disease defense and protein binding. Expression profiles of 90 C. bursa-pastoris genes were compared with those of the corresponding Arabidopsis genes and 64 genes showed similar expression profiles and the expression profiles of the rest 26 TDFs were different from those of the relevant Arabidopsis genes. Besides, some genes related to oxidative stress and ABA response were fiercely up-regulated during embryogenesis of C. bursa-pastoris according to RT-PCR.