We have constructed a cDNA library using poly(A)+ RNA from the stably transformed Marek's disease virus cell line MKT-1 and isolated cDNAs specific to the short internal repeat region of the BamHI-A fragment of the viral genome. Four distinct classes of cDNA were identified through sequence analysis of the 5' and 3' termini of each clone isolated, and a representative of each class was chosen for complete sequencing. These cDNAs were mapped on the basis of the genomic nucleotide sequence of this region, and a family of 3'-coterminal overlapping transcripts consisting of several highly spliced species, was identified. PCR was used to amplify specific regions of each cDNA, which were subcloned and used to generate riboprobes. These riboprobes hybridized to a variety of transcripts in poly(A)+ RNA fractions isolated from cells either lytically or latently infected with Marek's disease virus.