The structure of natural flax fibres is complex and hierarchical, consisting of multiple concentric layers that differ in composition and function. Naturally grown fibres show significant variation in structure that is likely to be responsible for the observed scatter in mechanical properties, most notably strength and stiffness. As flax fibres are being considered as an alternative reinforcement in composite materials to replace synthetic fibres, understanding the origins of property variability is a major objective of their study. High resolution synchrotron X-ray tomography (voxel size ~0.35 microns) on the TOMCAT station at the Swiss Light Source was used to create three-dimensional visualisation of the internal structure of individual flax fibres. Despite using the lowest X-ray energy available at the beamline (~8 keV), the contrast due to fibre absorption was quite low (about 2% absorption), creating significant challenges for data interpretation. The problem of data interpretation was exacerbated by small random movements of the sample ("jitter") caused by the air currents within the experimental hutch. The presence of phase contrast associated with the fibre edges allowed us to develop efficient algorithms for image post-processing for the purpose of re-alignment of the datasets ("de-jittering"). As a result, sharp and clear 3D visualisations of long segments of flax fibres were obtained. In addition to the well-known inner pore (lumen) running through the centre of the flax fibre, isolated cavities a few microns in diameter were found. The data also allows the assessment of fibre structure variation along its length. The data provides a valuable basis for attempting to cross-correlate these structural variations with the mechanical properties.