The Chelungpu fault, Taiwan, produced a northward propagating rupture on 21 September 1999 resulting in a Mw 7.6 earthquake with a ~90 km long N-S trending fault scarp. The mineralogic and physical character of the fault-related rocks within the Chelungpu fault zone, as measured at 9 sites along 70 km of the 1999 rupture trace, changes significantly along strike and with depth. The northern section of the Chelungpu fault has a 10 - 30 m-wide primary damage zone that is characterized by increased fracture density and alteration, but little microstructural damage to within 1 m from the main fault. The southern section of the Chelungpu fault has a 25 - 70 m wide primary damage zone that is characterized by increased fracture density and alteration, the presence of intensely sheared rock, and numerous secondary faults and gouge zones as far as 240 m from the main fault. The complexity of the damage zone, geochemistry, and clay mineralogy of the southern fault zone may reflect its relative maturity (~1 Ma) compared to the northern fault zone (~46 - 100 Ka). The major down-dip mineralogic variation is a transition from a significant amount of smectite in exhumed fault cores to little or no smectite in the fault core at sampled depths of 200 to 1000 m. This transition may be influenced by weathering processes at the surface, however co-seismic fluid flow may have a role in illite-smectite reactions. The composition of clays has important seismologic implications as clays play a role in fault weakening.