Apatites crystallized from different types of igneous rocks show significant variations in the abundances of some minor and trace elements. In this study, electron probe microanalysis and laser ablation inductively coupled plasma mass spectrometry were used to determine the concentrations of 25 minor and trace elements in apatite separated from three principal rock types of the Transhimalayan igneous plutonic suite: S-type granites, the I-type Gangdese batholith and post-collisional adakites. F, Mn, Sr and rare earth elements (REE) in apatite vary systematically with the composition of the host magma and thus have high potential as petrogenetic tracers. More specifically, the F and Mn contents of apatite can be used as an indicator of magma aluminosity or differentiation index. Combined with Sr and REE data, which show significant variations in apatite from different rock types, these elements are useful for constructing ‘discrimination diagrams’. This study also reveals that apatite has the capacity to retain geochemical information about the host magma through the course of magmatic evolution. Systematic variations of Sr and REE in apatite with bulk-rock aluminosity are the results of partition competition with pre-existing and coexisting major and accessory minerals in silicate melts, and thus are useful for more detailed investigations of petrogenetic processes such as fractional crystallization and magma mixing, which is signaled by inconsistent Eu anomalies, Sr abundances and REE patterns relative to bulk-rock compositions.