The New Schubert Edition is subdivided by genre and is generally arranged in chronological order within each genre.
One exception to this rule occurs with the lieder, where, for the first time since their initial publication, the opuses issued during Schubert’s lifetime (roughly one-third of his lieder) appear in the order chosen by the composer himself. Despite a widely held belief to the contrary, these opuses were not compiled on an arbitrary basis, but in accordance with clearly discernible principles. For further information see Walther Dürr, Die Lieder-Serie der Neuen Schubert-Ausgabe. Zu Schuberts Ordnung eigener Lieder, Musica 40 (1986), pp. 28–30 (Download here).
The current version of the editorial guidelines on which the New Schubert Edition is based can be downloaded here.
