Expanded trinucleotide repeats (TNRs) are the underlying cause of at least 23 human disorders including myotonic dystrophy type 1 (DM1), Huntington’s disease (HD), fragile X syndrome (FXS), and Friedreich’s ataxia (FRDA). Most TNR disorders are caused by expanded CAG/CTG repeats. Expansions occur when TNR tracts exceed a threshold of about 35 to 50 repeat units. Upon repeat expansion, pathogenic loci acquire characteristics typical of heterochromatin in affected patients. The chromatin modifications commonly found in TNR patients include increased levels of CpG methylation, enriched heterochromatic histone modifications such as histone 3 lysine 9 methylation, and a concomitant decrease of histone 3 and histone 4 acetylation. In FXS and FRDA patient cells, this heterochromatinization phenomenon is accompanied by changes in gene expression and three-dimensional (3D) chromatin folding at the mutated loci. However, no study to date has analyzed the 3D chromatin conformation of expanded CAG/CTG repeats. Given that pathogenic CAG/CTG repeat loci display local chromatin modifications similar to those found in FXS and FRDA, I tested the hypothesis that expanded CAG/CTG repeats alter the higher-order chromatin folding of disease loci and thereby affect the genetic instability of the underlying repeat tract. In this thesis, I tested this hypothesis directly by using a combination of experimental approaches to characterize the heterochromatic status of expanded DMPK and HTT alleles and obtain high-resolution chromatin interaction maps from DM1 and HD patient lymphoblastoid cell lines with circular chromosome conformation capture followed by high- throughput sequencing (4C-seq). The results presented here show that chromatin interactions remain unchanged upon repeat expansion at both heterozygous disease loci. Highly expanded CAG/CTG repeat tracts associated with increased DNA methylation and a loss of CTCF binding were not enough to alter the contacts established at the DMPK locus in patient cells. Furthermore, the ectopic insertion of an expanded CAG/CTG repeat tract did not alter the 3D chromatin contacts of a transgene in HEK293T cells. Given the results obtained in this thesis, I concluded that heterochromatic expanded CAG/CTG repeats do not significantly alter the higher-order chromatin conformation of disease-associated TNR loci. This supports a model wherein 3D chromatin organization does not contribute to the pathogenic mechanisms of DM1, HD, and possibly other expanded CAG/CTG loci in human disease.