We have performed a systematic temporal and spatial expression profiling of the developing mouse kidney using Compugen long-oligonucleotide microarrays. The activity of 18,000 genes was monitored at 24-hour intervals from 10.5dpc metanephric mesenchyme (MM) through to neonatal kidney and a cohort of 3600 dynamically genes identified. Early metanephric development was further surveyed by directly comparing RNA from 10.5 Vs 11.5 Vs 13.5dpc kidneys. These data showed high concordance with the previously published dynamic profile of rat kidney development (Stuart et al. 2001) and our own temporal data. Cluster analyses were used to identify gene-ontological terms, functional annotations, and pathways associated with temporal expression profiles. Genetic network analysis was also used to identify biological networks that have maximal transcriptional activity during early metanephric development, highlighting the involvement of proliferation and differentiation. Differential gene expression was validated using whole mount and section in situ hybridisation of staged embryonic kidneys. Two spatial profiling experiments were also undertaken. Metanephric mesenchyme (10.5dpc) was compared to adjacent intermediate mesenchyme to further define metanephric commitment. To define the genes involved in branching and in the induction of nephrogenesis, expression profiling was performed on ureteric bud (GFP+) FACS-sorted from HoxB7-GFP transgenic mice at 15.5dpc versus the GFP-negative mesenchymal derivatives. Comparisons between temporal and spatial data enhanced the ability to predict function for genes and networks. This study provides the most comprehensive temporal and spatial survey of kidney development to date and the compilation of these transcriptional surveys provides important insights into metanephric development that can now be functionally tested.