Significance A number of hereditary neurological and neuromuscular diseases are caused by the abnormal expansion of short tandem repeats, or microsatellites, resulting in the expression of repeat expansion RNAs and proteins with pathological properties. Although these microsatellite expansions may occur in either the coding or noncoding regions of the genome, trinucleotide CNG repeats predominate in exonic coding and untranslated regions while intron mutations vary from trinucleotide to hexanucleotide GC-rich, and A/AT-rich, repeats. Here, we use transcriptome analysis combined with complementary experimental approaches to demonstrate that GC-rich intronic expansions are selectively associated with host intron retention. Since these intron retention events are detectable in both affected tissues and peripheral blood, they provide a sensitive and disease-specific diagnostic biomarker.