Clay minerals are increasingly recognised as important controls on the state and mechanical behaviour of fault systems in the upper crust. Samples retrieved by shallow drilling from two principal slip zones within the central Alpine Fault, South Island, New Zealand, offer an excellent opportunity to investigate clay formation and fluid-rock interaction in an active fault zone. Two shallow boreholes, DFDP-1A (100.6 m deep) and DFDP-1B (151.4 m) were drilled in Phase 1 of the Deep Fault Drilling Project (DFDP-1) in 2011. We provide a mineralogical and textural analysis of clays in fault gouge extracted from the Alpine Fault. Newly formed smectitic clays are observed solely in the narrow zones of fault gouge in drill core, indicating that localised mineral reactions are restricted to the fault zone. The weak preferred orientation of the clay minerals in the fault gouge indicates minimal strain-driven modification of rock fabrics. While limited in extent, our results support observations from surface outcrops and faults systems elsewhere regarding the key role of clays in fault zones and emphasise the need for future, deeper drilling into the Alpine Fault in order to understand correlative mineralogies and fabrics as a function of higher temperature and pressure conditions.