Most proteins fold into their native structure through well defined pathways which involve a limited number of transient intermediates. Intermediates play a relevant role in the folding process; many diseases of genetic nature are in fact coupled with protein misfolding due to formation of stable, inactive intermediate species of the protein. This review deals with a number of diseases associated with protein misfolding and briefly describes the mechanism(s) responsible, at molecular level, for such pathologies. It is also considered the (native molten globule) transition, recently observed for some proteins, in which a native protein converts into a stable compact intermediate state able to carry out distinct physiological functions inside the cell. A non-native compact form of cyt c, for example, appears to have a role in the programmed cell death (apoptosis) after that the protein is released from the mitochondrion, and non-native forms of the same protein appear involved in some of the disorders attributed to amyloid formation.