The apo form of myoglobin has two non-native stable states that have been experimentally characterized. Investigation of these states has suggested possible folding pathways for myoglobin. We have performed molecular dynamics simulations on solvated isolated helices of myoglobin to investigate the relationship between the intrinsic stabilities of the isolated helices and the structure and folding pathway of apomyoglobin. Analyses of hydrogen bonding and fluctuations from simulations at 298 and 368 K are used to explore the relative stabilities of the helices of myoglobin. The ordering observed is A approximately G approximately H > B > E > F, which mirrors both the experimental equilibrium and kinetic data available for apomyoglobin. The experimental observation that a subdomain comprising helices A, G, and H is an important early intermediate and our result that these helices are the most stable suggest that the intrinsically more stable helices form early in the folding process and that this significantly influences the folding pathway.