The structure of viroids and the mechanism of structure formation were investigated by different methods. Results from gel analysis, partial degradation pattern, electron microscopy, dye binding, hydrodynamic studies, and temperature-jump kinetics were interpreted in a common structural and mechanistic scheme. Gel analysis, electron microscopy and kinetic investigations show that viroids may assume the native as well as metastable conformations under the same conditions. The native conformation is obtained by complete renaturation, i.e. slow cooling throughout the transition range (e.g. 52 to 48 ° C for potato spindle tuber viroid (PST viroid) in 0.01 m-sodium cacodylate, pH 6.8). In contrast, metastable conformations were trapped if viroids were redissolved in the cold from their ethanol precipitate or if they were denatured and cooled quickly. The native secondary structure of the recently sequenced PST viroid (Gross et al., 1978) was optimized for the free energy of base-pairing. The scheme agrees with that proposed by Gross et al. (1978), which was derived from chemical arguments. The extended structure does not undergo tertiary structure folding under a wide range of conditions, as was concluded from electron microscopy, sedimentation measurements and binding studies of ethidium bromide and a new dye specific for A · U pairs (2-(4′-aminophenyl)-5-(4′-methylpiperazin-1″yl)-benzirnidazol). Intermediate structures during viroid denaturation were analysed on theoretical and experimental grounds. The experimental data, in combination with the model calculations, show that all of the native base-pairs of viroids are dissociated in one highly co-operative main transition, and that during the same process very stable hairpins are formed that are not present in the native structure. The formation of stable hairpins induces a new type of long range cooperativity, which is responsible in part for the high co-operativity observed experimentally. This interpretation is in good agreement with kinetic results presented elsewhere (Henco et al., 1979). In order to understand the uniqueness of viroids, the structure and the conformational transitions of circular RNA molecules of the same base composition as PST viroids but with 359 nucleotides arranged randomly, were studied theoretically. Common viroid features, such as the number of base-pairs, the high co-operativity and the formation of very stable hairpins, are found to be improbable in such random sequences. It is concluded that various viroid species, although differing in nucleotide sequence, follow common principles of structure and structure formation.