Interest in polycyclic quinones derives not only from their photodynamic activity, but also from their possible application as antitumour and antiviral agents, in some cases as inhibitors of protein kinase C. A number of perylenequinones of natural origin are known, but the stereochemistry (they have a helical shape) and the interconversion process involving isomers with apparent opposed helicity, have not been sufficiently investigated. The conformational preference of the side-chains in the “1,12-bay” region, critical to generate the helical structure, was determined for perylenequinones 1–5 by the combined use of NOE data, of the two-bond and three-bond C,H and H,H coupling constants involving nuclei C-1, C-2, C-12b, C-15, 13-H and 14-H. As cercosporins 1, 2 and phleichromes 3, 4 possess a C₂ axis of symmetry, which reduces the number of available NMR parameters, an asymmetric derivative 5 (monoacetate of 1) was prepared. Quantitative NOE experiments on 5 gave information on the relative distance of the two chains and on the twist angle C(1)–C(2)–C(12a)–C(12) of the helix. The noranhydro compounds 6 and 7 were obtained by treatment with sulfuric acid of cercosporins 1, 2 and phleichromes 3, 4, respectively. The structure and the conformational preference of 6 and 7 were deduced by NMR at low temperature, by CD spectra and molecular modelling. The thermal inversion of the helix was studied by traditional kinetic experiments for 1–4 (the process is slow even at high temperature), by NOESY-exchange and dynamic NMR experiments for 6 and 7. The activation parameters ΔH^#, ΔG^#, and ΔS^# were thus obtained. The helix inversion process results tightly connected with the conformational change of the side-chains of the atropisomers, but not with the tautomeric state of the perylenequinone system.