Long non-coding RNAs (lncRNA) are a novel class of RNA molecule that are emerging as important regulators of gene transcription and post-transcriptional events. lncRNAs have been shown to regulate a broad variety of biological processes and are often located within regions of the genome that are associated with various diseases. Repetitive elements are a major component of lncRNA and their molecular functions in lncRNA are poorly understood. Here, I describe the evolution of Alu elements in lncRNA and mRNA. Alu elements are the most abundant transposable element in the human genome (more than 1 million copies) and their composition and evolution within lncRNA and mRNA differ significantly. These striking differences are correlated with their expression and suggest a common molecular function in lncRNA and mRNA.