This chapter presents analysis of ultraviolet-induced RNA–RNA cross-links. To obtain maximum information about local bonding patterns, the UV-induced cross-link must be mapped to the nucleotide level. Direct RNA analysis is needed. However, if cross-links are to be used only to determine which portions of the RNA are close together in the three-dimensional structure, indirect techniques, such as primer extension, may be employed. The mapping of an extensive series of RNA–RNA cross-links introduced into rRNA has led to a detailed three-dimensional picture of 16 S rRNA. While additional procedures are usually required to locate a UV-induced bond in a large RNA molecule, a cross-link in an RNA smaller than 1000 nt can often be detected directly by a change the cross-link makes in the characteristic pattern of ribonuclease-resistant oligonucleotides. Primer extension is useful for mapping cross-links, especially when employed in combination with direct RNA analysis.