Expansions of trinucleotide repeats encoding polyalanine tracts have been recognized as the cause of several diseases, predominantly congenital malformation syndromes. To date, nine genes with alanine tract expansions have been described. With the exception of PABPN1, which codes for a poly(A)-binding protein, all these genes encode transcription factors that play important roles during development. Recent in vitro and in vivo findings indicate that expansions of polyalanine tracts beyond a certain threshold result in protein misfolding, aggregation and subsequent degradation. Polyalanine tracts are relatively common in the genome and occur most frequently in transcription factors and other proteins with nuclear localization. The molecular role of alanine tracts is unknown, but their strong evolutionary conservation suggests the existence of potent functional or structural constraints.