In this article, microstructural changes in anatase titania (TiO2) nanotubes (NTs) upon electrochemical lithium (Li)-insertion/de-insertion using ex situ transmission electron microscopy (TEM) have been reported. TiO2 NT-arrays have been fabricated by coating the wall of the pores of the nanoporous anodic aluminum oxide (AAO) templates using atomic layer deposition (ALD). Anatase TiO2 NT-array based anode with the wall thickness of ∼14 nm shows a reversible discharge capacity of ∼175 mAh g−1 (i.e., Li-concentration (x) of ∼0.53) in the second discharge cycle. The NTs are structurally intact and maintain their high crystalline quality after many repetitions of charging and discharging. Reversible phase transformations from tetragonal (anatase) to orthorhombic (Li-titanate) polymorphs and back to tetragonal (anatase) in complete discharging/charging cycled TiO2 NTs are observed ex situ. Electrical conductivity of the NTs decreases a bit due to lithiation. Arrays of the anatase TiO2 NTs as anode in Li-ion secondary batteries show satisfactory cycle response and structural stability even after 50 cycles of charging/discharging.