CD46 (Membrane Cofactor Protein, MCP) is a transmembrane glycoprotein, which is expressed by all nucleated human cells whose purpose is to protect against autologous complement attack. In addition, CD46 can serve as a receptor for several viruses and bacteria and as a potent regulator of the inflammatory response by affecting T cell differentiation. Multiple isoforms of CD46 exist due to alternative splicing and are coexpressed in human cells in various patterns and expression levels. However, specific diseases have not been associated with isoform coexpression. We applied a nested RT-PCR method to investigate the coexpression pattern of CD46 splicing variants in otosclerotic and normal stapes footplate specimens. Using this method, we detected an altered isoform expression pattern and identified four novel CD46 splicing variants overexpressed in otosclerotic bone. This study is the first comprehensive report to provide evidence for disease associated alternative splicing of CD46.