This chapter discusses the involvement of genetic recombination in the instability of trinucleotide and tetranucleotide repeats. Genetic recombination was first demonstrated to be an important source of instability of minisatellites, a family of moderately sized (usually 6-100 bp), hypervariable repetitive elements. The expansion of microsatellite sequences at a particular locus in the human genome is a complex process, often initiated by establishing the group of "at-risk" alleles harboring the longest, uninterrupted repeat tracts (founder effect). These alleles have a high potential for large expansions in subsequent generations, leading to the phenotype changes. Somatic instability is the last, often disease-specific, step in the expansion process and occurs to various extents in different tissues. Genetic recombination may be involved in several events of microsatellite instability, such as hairpins, slipped structures, triplexes, sticky DNA structure, tetraplexes, and unwound DNA conformations that can interfere with various processes of DNA metabolism. The instability of the CTG·CAG repeats in the Machado-Joseph disease gene (MJDl) reveals that intermediate alleles arise through an interallelic gene conversion. © 2006 Elsevier Inc. All rights reserved.