Definitive diagnosis of neurodegenerative diseases (NDDs) relies on the neuropathological evaluation. NDDs are defined as disorders with progressive loss of neurons showing distinct anatomical distribution, and accordingly different clinical phenotypes. Recent research has identified a spectrum of immunohistochemically detectable proteins deposited in the central nervous system which serve as a basis for protein-based disease classification. Accordingly, diagnostic criteria and disease staging have been updated. Furthermore, it has become evident that there is considerable overlap between deposited proteins and pathologies. This review summarizes recent achievements in neuropathological diagnosis and classification of NDDs and recommends approaches to be used during the diagnostic procedure in practice, thus to serve as guideline for a common level of diagnostic quality.