Epstein-Barr virus (EBV) nuclear antigen (EBNA) was purified from the Burkitt lymphoma line Raji and its EBV DNA-binding properties were characterized. EBNA binding protected fragments of about 30 bp of B95-8 cell-derived EBV DNA from an excess of DNase I. Human anti-EBNA antibodies prevented DNA binding. Purified extracts from EBNA-negative cells did not protect EBV DNA against DNase I digestion. Mapping of the EBV DNA fragments protected from endonuclease (EcoRI, HindIII, SalI) digestion revealed many binding sites. Similar results were obtained following mixing of crude cell extracts and HindIII-digested fragments of EBV DNA and subsequent immunoprecipitation of the EBNA-DNA complex. In experiments involving the analysis of EBV DNA, fragments were protected from DNase I digestion by purified EBNA.