Amyloidosis comprises a group of diseases characterized by the deposition of insoluble protein fibrils in specific organs and includes several serious medical disorders, such as Alzheimer's disease, prion-associated transmissible spongiform encephalitis, and type II diabetes. Despite the structural dissimilarity between the soluble proteins and peptides, these fibrils exhibit similar morphologies under electron microscopy with a characteristic "cross beta-sheet" pattern examined by x-ray fiber diffraction experiments. Many studies have revealed that each of these diseases is associated to a specific protein that is partially unfolded, misfolded, and aggregated. However, the detailed structures of the causative agents and the toxicity mechanisms are less known. This review summarizes recent studies in the conformational disorders leading to aggregation; including which proteins potentially cause conformational diseases, the aggregation mechanisms of these proteins, and recent researches on the conformational changes using advanced experiments or molecular dynamics simulations. Finally, current drug designs towards these protein conformational diseases are also discussed. It is believed that the advances in basic understanding of the mechanisms of conformational changes as well as biological functions of these proteins will shed light on the development and design of potential interfering compounds against amyloid formation associated with protein conformational diseases.