A number of nuclear-encoded proteins are known to bind to the mitochondrial genome and may be involved in mitochondrial replication and in mitochondrial diseases. Mitochondrial diseases such as Kearns-Sayre syndrome (KSS) are flanked by common direct repeats. To study protein binding to these mitochondria DNA regions we used gel mobility shift binding assays. Proteins present in nuclear or in mitochondrial extracts from normal or KSS-derived fibroblasts bound to a 280-bp mitochondrial DNA fragment encompassing a deletion breakpoint in the mitochondrial genome. In addition, nuclear and mitochondrial protein bound to a nearby surrounding fragment and to a synthetic oligonucleotide with a related consensus DNA sequence. Southwestern blot analysis showed that the DNA binding ability resided in a 35-kDa protein. The amino terminal sequence of the 35-kDa protein was very similar to human high mobility group proteins. These results suggest that this protein may be involved in mitochondrial DNA deletions.