The island of Samos in the Aegean Sea exposes high-pressure metamorphic rocks of the Cycladic blueschist unit which are sandwiched between the mildly blueschist-facies Kerketas nappe below and the overlying non-metamorphic Kallithea nappe. Structural and metamorphic analysis shows that deformation can generally be divided into four main stages: (1) Eocene and earliest Oligocene ∼ESE–WNW-oriented nappe stacking (D 1 and D 2) associated with blueschist- and transitional blueschist–greenschist-facies metamorphism (M 1 and M 2). D 2 caused emplacement of the blueschist unit onto the Kerketas nappe indicating that thrusting occurred during decompression. (2) A subsequent history of Oligocene and Miocene horizontal crustal extension (D 3) before and after greenschist-facies metamorphism (M 3). Ductile flow during D 3 was characterized by a high degree of coaxial deformation but in general caused displacement of upper units towards the ENE. Nonetheless, the late-stage D 3 emplacement of the Kallithea nappe between 9 and 10 Ma had a top-to-the-NW/NNW sense of shear. (3) A short period of brittle E–W crustal contraction (D 4) occurred between <8.6 and ∼9 Ma. (4) A phase of N–S-directed normal faulting (D 5, <8.6 Ma to Recent). ESE–WNW-directed tectonic transport during D 1 through D 3 is in contrast to uniform NNE–SSW-directed tectonic transport in the adjacent Cyclades, Greece, as well as in the neighbouring Menderes Massif of western Turkey. Published paleomagnetic data reveal sinistral rotation between the Cyclades and western Turkey. We interpret this rotation as a consequence of differential extension between the severely extended Aegean and the moderately extended Menderes Massif during D 3. The onset of D 3 crustal extension is coeval with a marked change in the thermal structure. We propose that the thermal reorganization was associated with the retreat of the subduction zone towards the external Hellenides in the Early Oligocene and a subsequent increase in magmatic activity.