Binding specificity between fibroblast growth factors (FGFs) and their receptors (FGFRs) is essential for mammalian development and is regulated primarily by two alternatively spliced exons, IIIb (''b'') and IIIc (''c''), that encode the second half of Ig-like domain 3 (D3) of FGFRs. FGF7 and FGF10 activate only the b isoform of FGFR2 (FGFR2b). Here, we report the crystal structure of the ligand-binding portion of FGFR2b bound to FGF10. Unique contacts between divergent regions in FGF10 and two b-specific loops in D3 reveal the structural basis by which alternative splicing provides FGF10-FGFR2b specificity. Structure-based mutagenesis of FGF10 confirms the importance of the observed contacts for FGF10 biological activity. Interestingly, FGF10 binding induces a previously unobserved rotation of receptor Ig domain 2 (D2) to introduce specific contacts with FGF10. Hence, both D2 and D3 of FGFR2b contribute to the exceptional specificity between FGF10 and FGFR2b. We propose that ligand-induced conformational change in FGFRs may also play an important role in determining specificity for other FGF-FGFR complexes. Binding specificity between FGFs and FGFRs is critical for the proper regulation of FGF signaling. The physiological significance of FGF-FGFR specificity is best demonstrated in Apert syndrome, a severe craniosynostosis syndrome, where point mutations in FGFR2 alter ligand binding affinity and specificity (8-10). Alternative splicing of FGFR mRNA is the main mechanism by which FGFRs with different ligand-binding profiles are generated. In FGFR1 to -3, D3 is encoded by the invariant exon IIIa followed by one of two alternative exons, IIIb (''b'') or IIIc (''c''). This alternative splicing event is regulated in a tissue-specific fashion with b expression restricted to epithelial lineages and c to mesenchymal lineages (11)(12)(13)(14). Most FGFs activate more than one FGFR. The FGF7 subfamily is unique among FGFs because its members (FGF7, FGF10, and FGF22) are expressed exclusively by mesenchyme and interact specifically with the b splice variant of FGFR2 (FGFR2b) resident in overlying epithelium (15-17).FGF7 and FGF10 bind FGFR2b with similar high affinity and compete with each other for this binding (18,19). However, striking phenotypic similarities between the FGF10 and FGFR2b knockout mice have established FGF10 as the predominant ligand for FGFR2b in developmental patterning and organogenesis. Both FGFR2b-null and FGF10-null mice die at birth and show agenesis of the lungs and limbs, whereas FGF7-null mice are viable and have normal lungs and limbs (16,(20)(21)(22).The exceptional specificity between the FGF7 subfamily and FGFR2b, together with the pivotal role of FGF10-FGFR2b signaling during development, makes the FGF10-FGFR2b complex an ideal model system for deciphering the structural determinants of FGF-FGFR binding specificity. In this report, we describe the crystal structure of the FGF10-FGFR2b complex and confirm the structural findings by mutational analysis. FGF10-FGFR2b specificity incorporate...