This chapter discusses structural features of triplet repeats in transcripts relevant to the more prominent role of RNA in the pathogenesis of triplet repeat expansion diseases (TRED). The number of different transcripts harboring triplet repeats but also their expression levels in different cell types and tissues influence the cellular balance of the repeat containing transcripts and repeat binding proteins, which might be important for the mechanism of RNA-mediated pathogenesis. Bearing that in mind, the available gene expression data have been analyzed, by using tools of bioinformatics, to characterize the abundance of a large group of the repeat containing transcripts in different human tissues: brain, prostate, liver, kidney, pancreas, and lung. The CNG repeat containing transcripts were shown to belong to moderate and low abundance classes. The CNG repeat regions in transcripts may form hairpin structures of different molecular architecture. Moreover, hairpins composed of a lower number of repeats but well-stabilized by the flanking sequences may exert effects similar to those composed of a larger number of repeats, but lacking any additional stabilization. © 2006 Elsevier Inc. All rights reserved.