This article examines Newton’s method of induction and its connection to methodological atomism. The article argues that Newton’s Rule III for the Study of Natural Philosophy is a criterion for isolating the primary qualities of the atomic parts; in other words, it interprets Rule III as a transductive inference. It is shown that both the standard inductive and invariance interpretations of Rule III can be subsumed under the transductive view, although the invariance criterion is reinterpreted; by qualities “that cannot be (...) intended or remitted,” Newton means qualities that are invariant under changes in the configuration of the atomic parts. (shrink)