The most frequent form of X-linked deafness, deafness type 3 (DFN3) is characterized by temporal bone abnormalities, stapes fixation, and, in most cases, a mixed type of deafness. The physical fine mapping of (micro)deletions associated with classic DFN3 enabled the positional cloning of the underlying gene, POU3F4. Missense mutations identified in the POU3F4 gene of DFN3 patients are conspicuously clustered in the 3-helix of the POU homeodomain, suggesting that missense mutations outside the POU domains result in a different phenotype. Surprisingly, the POU3F4 gene was situated outside several microdeletions associated with DFN3 and detailed analysis of the proximal region led to the identification of several DFN3-associated microdeletions 900 kb upstream of POU3F4. In addition, we identified a DFN3-associated paracentric inversion (q21.1q21.31) in which one of the inversion breakpoints is located 170 kb proximal to POU3F4. The smallest proximal deletion, which is contained in all other proximal deletions except one, merely spans 8 kb and contains non-transcribed but highly conserved sequences. These findings might be explained by the presence of a long-range transcriptional regulation element, possibly an enhancer, 900 kb proximal to POU3F4. Spatiotemporal expression studies indicate that POU3F4 does not only play an important role in otogenesis, but also in brain, kidney and muscle development. In addition, POU3F4 expression was detected in the adult mouse heart and pancreatic -cells. The absence of overt clinical features in DFN3 patients outside the temporal bone suggests that there is a high degree of functional redundancy among different members of the POU domain superfamily.