Models for the disease-associated expansion of trinucleotide repeats involve the participation of alternative DNA structures during replication, repair, or recombination. CAT or AGG interruptions within the (CAG)n or (CGG)n repeats of SCA1 or FRAXA, respectively, confer increased genetic stability to the repeats. In this study, we report the formation of slipped strand structures (S-DNA) using genomic sequences containing pure and interrupted SCA1 and FRAXA repeats having lengths above and below the genetic stability thresholds. S-DNA forms within the repeats during annealing of complementary strands containing equal lengths of repeats. Increased lengths of pure repeats led to an increased propensity for S-DNA formation. CAT or AGG interruptions have both quantitative and qualitative effects upon S-DNA formation: they decrease the total amount of slipped structures as well as limit the specific isomers formed. This demonstrates a unifying inhibitory effect of interruptions in both (CAG)n and (CGG)n tracts. We also present transmission stability data for SCA1 and FRAXA alleles spanning the thresholds and compare these with the ability to form slipped structures. The effect of both the length and purity of the repeat tract on the propensity of slipped structure formation correlates with their effect on genetic instability and disease, suggesting that S-DNA structures may be models for mutagenic intermediates in instability.