In muscle biopsies from patients with inclusion body myositis (IBM), multiple sites were found in many muscle fibers that bound single-stranded but not double-stranded DNA without sequence specificity, as exemplified by several different cDNA probes. This activity was attributable to a protein, because it was abolished by proteases but not by RNAse. Most of the sites of binding were myonuclei, whereas some were rimmed vacuoles, which probably result from nuclear breakdown. No comparable binding was seen in 27 control biopsies. A number of human and viral single-stranded DNA binding proteins exist but our data does not identify the protein responsible for DNA binding in IBM. Our findings reinforce the supposition that nuclear damage plays a basic role in the pathogenesis of IBM.