Friction stir welds were made in 6 mm thick plate in the mill annealed and beta annealed conditions using a commercially pure tungsten pin-tool. A detailed characterization of the microstructure, using transmission and scanning electron microscopy, is presented here as a complement to previous texture analysis (using orientation imaging microscopy) with the aim of describing the evolution of microstructure during the FSW of titanium alloys. In both material conditions, the stir zone is characterized as a colony structure with a refined (10 mum) prior beta grain size that developed during the relatively slow cooling from above the beta transus temperature. The beta grain size in the stir zone does not appear to be related to the microstructure prior to welding but rather to the extensive local deformation in this region and the relatively short dwell time above the beta transus, both of these a factor in preventing beta grain growth. The cooling rate from the beta transus was slow enough to cause formation of grain boundary alpha along the prior beta grain boundaries but rapid enough to cause stacking fault formation on basal planes in the alpha phase. The thermomechanically affected zone, TMAZ, contains a large amount of fine (I mum) equiaxed alpha, the origin of which is still unknown and for which possible explanations will be presented. The thermo-mechanical history of the TMAZ of the mill annealed material caused the precipitation secondary alpha. Results will be presented with discussion focused on the combined effects of deformation and phase transformations.