The structure of microcrystalline cellulose (MCC) made by mild acid hydrolysis from cotton linter, flax fibres and sulphite or kraft cooked wood pulp was studied and compared with the structure of the starting materials. Crystallinities and the length and the width of the cellulose crystallites were determined by wide-angle X-ray scattering and the packing and the cross-sectional shape of the microfibrils were determined by small-angle X-ray scattering. The morphological differences were studied by scanning electron microscopy. A model for the changes in microfibrillar structure between native materials, pulp and MCC samples was proposed. The results indicated that from softwood or hardwood pulp, flax cellulose and cotton linter MCC with very similar nanostructures were obtained with small changes in reaction conditions. The crystallinity of MCC samples was 54-65%. The width and the length of the cellulose crystallites increased when MCC was made. For example, between cotton and cotton MCC the width increased from 7.1 nm to 8.8 nm and the length increased from 17.7 nm to 30.4 nm. However, the longest crystallites were found in native spruce wood (35-36 nm).