X-ray CT images usually show artefacts due not only to physical effects -e.g., beam hardening-, but also to misalignments that remain after mechanical calibration. These artefacts become particularly noticeable in the case of high spatial resolution systems and in hybrid systems, such as PETCT, SPECT-CT scanners, which rely on a correct registration of emission and CT data. Hence, slight mechanical misalignments affect the quality of the CT images and any attenuation correction methods or further quantification based on them. We implemented a computer simulator of these artefacts on a conebeam, flat-panel based micro-CT scanner. Using this simulator, we studied the effect of these different misalignments (pitch and roll tilts, skew and shifts) on reconstructed images.