Neurodegenerative diseases are characterized by the deposition in a variety of tissues of specific proteins as aggregated species that share a distinctive fibrillar or amorphous structure. Although amyloid inclusions (deposits) are predominantly proteinaceous, careful examination of diseases tissues has revealed the presence of a significant quantity of other species, such as nucleic acids and/or polysaccharide species, associated with the inclusions. Recently, both DNA and RNA have been shown to be able to stimulate formation of fibrillar or amorphous aggregates in vitro by alpha-synuclein, tau protein and prion proteins, and to act as a template for accelerating the aggregation of copper/zinc superoxide dismutase. Although the specificity and nature of interactions between disease-linked proteins and nucleic acids are controversial, the sites of interactions involved should be the positively charged surface motifs on the proteins. This review will mainly highlight the important progress in studies on the nucleic acid-induced structural conversions and aggregation of the proteins linked to neurodegenerative diseases. Thereby, we attempt to understand biological and pathological implications of nucleic acid-induced protein aggregation.