The use of the complete DNA sequence for the Marek’s disease virus (MDV) serotype 1 vaccine strain CVI988 Rispens in comparative genomic studies with virulent strains of MDV has revealed the presence of a number of insertions, deletions and single-nucleotide polymorphisms. In this study, we investigated a SNP in the H/ACA box of the viral RNA subunit of telomerase (vTR). We sequenced vTR from four different batches of CVI988 vaccine originating from a single commercial company. The A-to-G mutation defining the SNP in the H/ACA box of CVI988 vTR was present in only some of the batches. Thus, although this mutation affects CVI988 vTR function, it is not shared by all CVI988 isolates and may be a stochastic rather than causative event in CVI988 attenuation.