The development of fatigue damage in a glass fibre modified layer-to-layer three dimensional (3D) woven composite has been followed by time-lapse X-ray computed tomography (CT). The damage was found to be distributed regularly throughout the composite according to the repeating unit, even at large fractions of the total life. This suggests that the through-thickness constraint provides a high level of stress redistribution and damage tolerance. The different types of damage have been segmented, allowing a quantitative analysis of damage evolution as a function of the number of fatigue cycles. Transverse cracks were found to initiate within the weft after just 0.1% of life, followed soon after (by 1% of life) by longitudinal debonding cracks. The number and extent of these multiplied steadily over the fatigue life, whereas the spacing of transverse cracks along with weft/binder debonding saturated at 60% of life and damage in the resin pockets occurred only just before final failure.