The myotonic dystrophy (DM) mutation has been identified as an unstable, expanded (CTG)n repeat in the 3' untranslated region of a gene designated DM protein kinase (DMPK). Both decreased and increased levels of mutant DMPK mRNA as well as decreased levels of protein have been variously reported and invoked to explain disparate molecular bases of this dominantly inherited disease. Most recently, increased nucleosome binding to such expanded repeats has been interpreted as support for transcriptional repression. A quantitative allele-specific RT-PCR procedure was developed and applied to a spectrum of patient tissue samples and cell lines. Equal levels of unprocessed pre-mRNA were produced by the wildtype (+) and disease (DM) alleles in skeletal muscle and cell lines of heterozygous DM patients. Thus, any increased nucleosome binding had no effect at the level of transcriptional initiation and transcription of the mutant DMPK locus. In contrast, processed mRNA levels from the DM allele were reduced relative to the+allele as the size of the expansion increased. The unstable repeat, therefore, impairs post-transcriptional processing of DM allele transcripts. This phenomenon has profound effects on overall DMPK locus steady-state transcript levels in cells missing a wildtype allele and does not appear to be mediated by imprinting, decreased mRNA stability, generation of aberrant splice forms, or absence of polyadenylation of the mutant allele.