SALL1 is a mammalian homologue of the Drosophila region-specific homeotic gene spalt (sal) and heterozygous mutations in SALL1 in humans lead to Townes-Brocks syndrome. We isolated a mouse homologue of SALL1 (Sall1) and found that mice deficient in Sall1 die in the perinatal period with kidney agenesis. Sall1 is expressed in the metanephric mesenchyme surrounding ureteric bud and homozygous deletion of Sall1 results in an incomplete ureteric bud outgrowth. Therefore, Sall1 is essential for ureteric bud invasion, the initial key step for metanephros development. We also generated mice in which a green fluorescent protein (GFP) gene was inserted into the Sall1 locus and we isolated the GFP-positive population from embryonic kidneys of these mice by fluorescence-activated cell sorting (FACS). We then compared gene expression profiles in the GFP-positive and -negative population using microarray analysis, followed by in situ hybridization. We detected many genes known to be important for metanephros development, and genes expressed abundantly in the metanephric mesenchyme. We also found groups of genes which are not known to be expressed in the metanephric mesenchyme. Thus a combination of microarray technology and Sall1-GFP mice is useful for systematic identification of genes expressed in the developing kidney.