Instability of trinucleotide repeat sequences such as (CAG)•(CTG) have been linked to more than 14 human disorders, including Huntington disease and myotonic dystrophy. Repeat instability is thought to arise through the escaped/failed or aberrant repair of slipped DNA repeat structures. Since many trinucleotide repeat disorders display a neurological phenotype, we sought to investigate whether slipped CAG and CTG repeat structures could be repaired by cell extracts of the human neuroblastoma cell line, SH-SY5Y. Extracts of undifferentiated and differentiated SH-SY5Y cells were able to repair slipped CAG and CTG repeat structures in a nick-directed fashion, with no quantitative or qualitative differences in repair efficiencies between undifferentiated and differentiated SH-SY5Y extracts. However, repair efficiency was influenced by nick polarity as structures with 5' nicks displayed higher repair efficiencies than those with 3' nicks. Such repair influences may help to explain the different mutation patterns seen at various genetic loci and tissues.