Alternative splicing of pre-mRNA is one of the main mechanisms regulating gene expression that generates multiple transcripts from one gene. The review considers the specific role that intramolecular secondary structures arising through the interaction of distant complementary regions of introns play in regulating alternative splicing. Examples where aberrant splicing associated with hereditary disorders is corrected by altering the pre-mRNA secondary structures are described. The advances and prospects in whole transcriptome analysis of structured RNA regions and studies of their role in regulating alternative splicing are discussed.