Fibrillin microfibrils endow mammalian connective tissues with elasticity and play a fundamental role in the deposition of elastin. The microfibrils are 57 nm periodic supramolecular protein polymers with a mass of 2.5 MDa per repeat. The organisation of molecules within a microfibril is still open to debate and structural studies are only just starting to unravel this issue. The contribution of microfibril associated proteins to microfibril ultrastructure and whether there are any tissue specific differences in microfibril structure is still unknown. Therefore, we have used low dose electron microscopy, single particle image analysis and atomic force microscopy to study the structure of fibrillin microfibrils from different tissues. EM images of microfibrils from aorta, ciliary zonules and vitreous humor were collected and more than 500 microfibril repeats from each sample were subjected to averaging. Averages from each sample were analysed using axial stain exclusion patterns and difference images to detect any variations between them. The overall morphology of fibrillin microfibrils was conserved between tissues and there were only very minor differences in the bead and shoulder region of microfibrils. These data suggest that the structure of isolated microfibrils represents the fibrillin scaffold, and either microfibril associated molecules are lost on purification or play only a minor role in microfibril structure.