Huntington disease (HD) is caused by a CAG trinucleotide expansion in the huntingtin gene (HTT), which codes for the pathologic mutant HTT (mHTT) protein. Here, the authors engineered zinc finger protein transcription factors (ZFP-TFs) to target the CAG repeat and selectively repress levels of mHTT. In patient-derived fibroblasts and neurons, ZFP-TFs selectively repressed >99% of HD-causing alleles while preserving expression of >86% of normal alleles. This allele selective approach is essential as normal HTT is thought to have an important role in brain function.