The late 19th century debate among German-speaking physicists about theoretical entities is often regarded as foreshadowing the scientific realism debate. This paper brings out differences between them by concentrating on the part of the earlier debate that was concerned with the conceptual consistency of the competing conceptions of matter---{}mainly, but not exclusively, of atomism. Philosophical antinomies of atomism were taken up by Emil Du Bois-Reymond in an influential lecture in 1872. Such challenges to the consistency of atomism had repercussions within (...) the physics community, as can be shown for the examples of Heinrich Hertz and Ludwig Boltzmann. The latter developed a series of counter-arguments, culminating in an ingenious attempt to turn the tables on the critics of atomism and prove the inconsistency of non-atomistic conceptions of nature. Underlying this controversy is a disagreement over specific goals of physical research which was considered crucially relevant to the further course of physical inquiry. It thereby exemplifies an attitude towards the realism issue that can be contrasted with a different, more neutral attitude of construing the realism issue as merely philosophical and indifferent with respect to concrete research programs in physics, which one also occasionally finds expressed in the 19th century controversy and which may be seen as the prevailing attitude of the 20th century debate. (shrink)