Only a small portion of the total RNA transcribed in human cells becomes mature mRNA and constitutes the human transcriptome, which is context-dependent and varies with development, physiology and pathology. A small fraction of different repetitive sequences, which make up more than half of the human genome, is retained in mature transcripts and shapes their function. Among them are short interspersed elements (SINEs), of which Alu sequences are most frequent, and simple sequence repeats, which come in many varieties. In this review, we have focused on the structural and functional role of Alu elements and trinucleotide repeats in transcripts.