Trinucleotide repeat expansions have been associated with many neurodegenerative diseases, developmental disorders and muscular dystrophies. Among those triplet repeat expansions, polyalanine tract elongations are associated with early developmental abnormalities with the exception of OPMD, a late onset muscular dystrophy. This review presents an overview of recent advances on the molecular mechanisms underlying the group of polyalanine diseases and provides insights into the pathological impact of polyalanine tract expansion on protein dysfunction. While hydrophobic polyalanine tracts in the normal range are considered to be flexible spacers that confer stability and flexibility to the protein three-dimensional conformation, expanded polyalanine repeats are thought to destabilize the native conformation of the protein and alter protein levels and activity. Protein dysfunction following polyalanine expansion has been reported to cause transcriptional dysregulation which may delay early developmental processes or induce cytotoxicity in polyalanine disease models.