The Santorini Volcanic Complex (SVC) is an area in the Southern Aegean (Greece) which has been characterized by low seismicity rates for the last decades, especially in the Santorini Caldera where they have been very low until 2010. This pattern changed completely in February 2011, when intense microseismic activity was initiated within the Caldera. During the manual analysis of the events, the shear-wave splitting phenomenon was observed, revealing the existence of an anisotropic upper crust in the SVC area. A detailed anisotropy study has been conducted using 231 events within the shear-wave window that fulfilled the selection criteria. The polarization direction of the fast shear-wave, the time-delay between the two split shear-waves and the source polarization direction were calculated after visual inspection, using both the polarigram and the hodogram representations. This procedure, applied for eight local stations, resulted in the determination of 340 splitting parameters. The obtained mean anisotropy directions are not homogeneous, revealing a complex regime in the activated area. Nevertheless, these results are explained by the APE model, related to the stress-sensitive behavior of fluid-saturated microcracked rocks. A detailed analysis of the temporal evolution of both the time-delay and anisotropy direction was carried out. The time-delays measured in the “band-1” window exhibit gradual increase and sudden drop that can be related to imminent bursts of seismicity, as well as to the major Mw=5.1 and 5.2 events which took place about 40km SW of Santorini on 26 and 27 January 2012, respectively. On the other hand, no significant temporal variations or 90° flips of the Sfast polarization direction were observed.