The size of the Epstein-Barr virus (EBV) nuclear antigen (EBNA) in cells infected with different EBV isolates varies directly with the size of the EBV triplet repeat array, IR3. The isolate with the largest IR3 fragment has approximately 170 more codons than the isolates with the smallest IR3 fragment; it encodes an EBNA which is approximately 17,000 daltons larger than the smallest EBNA. The EBV IR3 encodes part of a 2-kilobase exon of a latently infected cell messenger RNA which must be translated into a repetitive amino acid domain of EBNA.