Chromosomes of many eukaryotic organisms including humans contain a large number of repetitive sequences. Several types of commonly present DNA repeats have the capacity to adopt hairpin and cruciform secondary structures. Inverted repeats, AT- and GC-rich micro- and minisatellites, comprising this class of sequence motifs, are frequently found in chromosomal regions that are prone for gross rearrangements in somatic and germ cells. Recent studies in yeast and mammals indicate that a double-strand break occurring at the sites of unstable repeats can be an initial event in the generation of chromosome rearrangements. The repeat-induced chromosomal instability is responsible for a number of human diseases and has been implicated in carcinogenesis. In this review, we discuss the molecular mechanisms by which hairpins and cruciforms can trigger chromosomal fragility and subsequent aberrations in eukaryotic cells. We also address the relationship between secondary structure-mediated genetic instability and human pathology.