Kidney development has often served as a model for epithelial-mesenchymal cell interaction where the branching epithelium of the ureteric bud induces the metanephrogenic mesenchyme to form epithelial nephrons. In a screen for genes differentially expressed during kidney development, we have identified a novel gene that is dynamically expressed in the branching ureter and the developing nephrons. It was designated Emu1 since it shares an N-terminal cysteine-rich domain with Emilin1/2 and Multimerin. This highly conserved EMI domain is also found in another novel protein (Emu2) of similar protein structure: an N-terminal signal peptide followed by the EMI domain, an interrupted collagen stretch, and a conserved C-terminal domain of unknown function. We identified two further secreted EMI domain proteins, prompting us to compare their gene and protein structures, the EMI domain phylogeny, as well as the embryonic expression pattern of known (Emilin1/2, Multimerin) and novel (Emu1/2, Emilin3, Multimerin2) Emu gene family members. Emu1 and Emu2 not only show a similar structural organization, but furthermore a striking complementary expression in organs developing through epithelial-mesenchymal interactions. In these tissues, Emu1 is restricted to epithelial and Emu2 to mesenchymal cells. Preliminary biochemical analysis of Emu1/2 confirmed that they are secreted glycoproteins which are attached to the extracellular matrix and capable of forming homo- and heteromers via disulfide bonding. The widespread, but individually distinct expression patterns of all Emu gene family members suggest multiple functions during mouse embryogenesis. Their multidomain protein structure may indicate that Emu proteins interact with several different extracellular matrix components and serve to connect and integrate the function of multiple partner molecules.