α-1,4-linked oligogalacturonides (OGs) are pectic fragments of plant cell walls that are able to induce defence and developmental responses. To understand plant responses to OGs at the transcriptional level, changes in gene expression were examined using oligonucleotide-based microarrays that cover almost the entire Arabidopsis transcriptome. In suspension-cultured Arabidopsis thaliana (L.) Columbia hypocotyl cells, approximately 4% of the total transcriptome exhibited significant change in abundance in response to treatment with OGs for 2 h. Steady-state changes in the abundance of transcripts encoding stress- and disease-related proteins, signalling components, and transcription factors were particularly noteworthy. As in other plant cell types, OGs elicit a rapid, but transient, elevation in cytosolic free Ca2+. The Ca2+ transient can be abolished by the protein kinase inhibitor 4,5,6,7-tetrabromobenzotriazole (TBB) and by the Ca2+ channel inhibitor La3+, thereby facilitating a distinction between Ca2+-dependent and -independent transcriptional responses. Among the 244 transcripts that were up-regulated by OGs, the response of 93 (38%) was selectively sensitive to abolition of the Ca2+ transient. These OG-up-regulated, Ca2+-dependent transcripts included two noteworthy classes, the first comprising genes involved in cell wall modification following pathogen attack, and the second consisting of genes involved in the biosynthesis of jasmonate and C6 volatile compounds. These results support the notion of an important role for cytosolic Ca2+ signalling in jasmonate biosynthesis following OG perception. Promoter analysis of OG-induced, inhibitor-sensitive and -insensitive genes identified several putative cis-elements that might be involved specifically in Ca2+-dependent transcriptional regulation.