Subvolcanic systems are characterized by complex combinations of intrusive units (dykes, sills, saucer-shaped sills, cone sheets, etc.) for which genetic relationships are unclear. This chapter explains how whole-rock geochemistry may be used to resolve the genetic relationships of such subvolcanic (and volcanic) systems. We start with a short introduction of the geochemical fingerprinting method with particular emphasis on the statistical refinement method called Forward Stepwise-Discriminant Function Analysis (FS-DFA). Combined with field mapping and structural analysis, geochemical fingerprinting based on major and trace elements and isotope ratios, is a very powerful tool to distinguish between igneous units (lavas, sills, dykes) with subtle (or not so subtle) geochemical differences. Different geochemical fingerprinting or signatures indicate derivation from distinct magma batches. The results from FS-DFA analyses may be used to reveal genetic relationships between geological units, or lack of such, which again may be used to throw light on subvolcanic plumbing systems, the feeding system in sill-dyke complexes, as well as other problems. The method is illustrated by studies of the Golden Valley Sill Complex in the Karoo Basin (South Africa).