Abstract: Microtubules are usually depicted as almost perfect polymers of the tubulin heterodimer that shares homotypic interactions between its subunits, except at a unique region called the 'seam'. To address this paradigm, we decorated microtubules with kinesin motor domains, performed 3D reconstructions by cryo-electron tomography, and developed a segmented sub-tomogram averaging strategy to address their structural heterogeneity. We found that when assembled from purified tubulin, microtubules can contain several seams whose number and location vary along their length, leaving holes within their shaft. Those assembled in Xenopus egg cytoplasmic extracts are much more homogeneous, but still incorporate variations in seam number and location, suggesting a tightly regulated process in a cytoplasmic environment. These observations prompted us to propose the concept of 'microtubule structural instability' that may be involved in their particular dynamic behavior known as 'microtubule dynamic instability'. We anticipate that microtubules associated proteins such as end-binding proteins could exploit this unique structural property to finely tune their dynamics in cells.