Lately it has been demonstrated that natural fibres may be an environmentally superior alternative for, e.g., glass fibres. In order to estimate properties of composite materials made of natural fibres, models designed for synthetic fibres are often used. The models usually do not account for irregularities in the material, e.g., suboptimal fibre orientation due to the twisting angle of fibres in yarns. Use of models without taking those features into account might lead to unreliable results. Methods to quantify the microstructural properties of natural fibre composites with X-ray microtomography and three-dimensional image analysis are demonstrated in this work. The methods are applied to flax fibre composites made from three different kinds of pre-forms. Microstructural parameters estimated with the methods are used in micromechanical models for the stiffness of the composite. Comparison between rule-of-mixtures and classical laminate theory is made, highlighting the requirement for accurate parameter estimation and use of a model that accounts for significant structural features of the material.