Hairy/Enhancer of Split (Hes) genes encode transcriptional repressors that function as downstream targets of activated Notch receptors in cell fate decisions during tissue development. During nephrogenesis, multiple Notch pathway genes are co-expressed in multi-potent epithelial progenitors (i.e. pre-tubular aggregates), but demonstrate distinct expression patterns in early nephrons (i.e. S-shaped bodies), suggesting that Notch signaling functions in patterning epithelial cell fate during nephron morphogenesis. To define the spatial activation of the Notch pathway in developing nephrons, we analyzed the expression of Hes1 and Hes5 by mRNA in situ hybridization in cryosections of developing kidneys, and compared their spatiotemporal expression with the expression of other Notch pathway genes in nephron progenitors. Hes1, and to a lesser extent Hes5, were expressed in pre-tubular aggregates and comma-shaped bodies of embryonic day (E) 13.5 and newborn kidneys. In S-shaped bodies, Hes1 expression was detected in the middle part which gives rise to the proximal tubule, but also extended into the lower and upper parts which give rise to the glomerulus and distal tubule, respectively, and was similar to the proximal-distal expression patterns for Notch1 and Jagged1 in these nephrogenic structures. In contrast, strong Hes5 expression was restricted to the middle segment of S-shaped bodies, and resembled Delta-like 1 expression. These data show that Hes1 and Hes5 expression are independently regulated along the proximal-distal axis of the developing nephron. Consequently, the differential, spatial regulation of Hes1 and Hes5 gene expression by the Notch signaling pathway in developing nephrons may be a mechanism for patterning cell fate decisions during nephron morphogenesis.