Music theory has increasingly been attempting to find points of conjunction between the analytical methods of Heinrich Schenker and those of Arnold Schoenberg. However, the move toward a reconciliation has encountered obstacles because of the uneven development of the two schools and differences in the philosophical background of their procedures. The present article focuses on these differences through an examination of three standard examples: the first movements of Beethoven's sonatas op. 2 no. 1, op. 10 no. 1 and op. 57. The comparison of Schenker's analyses in Der Tonwille and Der freie Satz with those of Schoenberg, Webern, Rufer and Ratz shows that the disagreement principally concerns musical form and the functions of its components. The differences can finally be traced back to two opposite paradigms: music as nature and music as language.