The vertebrate kidney develops through a series of mesenchymal-epithelial interactions between the ureteric bud and the metanephrogenic mesenchyme to form nephrons and the collecting system, which are both embedded in the renal interstitium. The interstitial stromal cells are an essential prerequisite for regular kidney development, but their origin and function is poorly understood. They are found in the kidney periphery and the medulla and are likely derived from the kidney mesenchyme and/or from migrating neural crest cells. During late kidney development, stromal cells are lost through massive apoptosis. We have identified a novel marker of kidney stroma cells, Snep (stromal nidogen extracellular matrix protein), that is additionally expressed in mesenchymal cells of other embryonic tissues and within the nervous system. Of interest, Snep transcripts are also found at sites of embryonic apoptosis. Furthermore, comparative expression analysis of kidney stroma markers suggests that Snep is expressed in a specific subpopulation of stromal cells and may provide environmental cues to support regular development.