Composite materials with 3-dimensional (3D) reinforcement were manufactured and corresponding simulation models were created in parallel. The used simulation approach has earlier been shown to produce close to authentic geometrical representation of the yarn architecture in 3D reinforcement. It is shown that although the as-woven reinforcement pattern can be modelled quite reliably, significant distortion from the nominal fibre arrangement might take place later in manufacturing, primarily related to compression during moulding. Such effects have earlier received significant attention for composites with 2-dimensional reinforcement but not as much for their 3D counterparts. The yarns in the real and the simulated materials are studied and compared, and some of the discrepancies and the mechanisms behind are discussed. The distortions are partly attributed to the relatively sparse weave that allows yarns oriented in the through-thickness direction, in particular, to deviate from their original positions.