Microcomputed tomography (micro-CT) is a frequently used imaging tool for a wide spectrum of in-vivo mouse models in basic and translational research. To allow an accurate interpretation of micro-CT images, high spatial resolution is necessary. However, this may also lead to a high radiation exposure of the animals. Therefore, animal welfare requires exact information about the expected radiation doses for experimental planning. To gain this, a mouse cadaver was herein used for micro-CT analyses under different conditions. For each radiation dose measurement, the cadaver was labeled with thermoluminescent dosimeter chips around the thoracic skin surface. Micro-CT scans of the thorax were performed with spatial resolutions of 35 µm, 18 µm and 9 µm in combination with Al0.5, Al1.0, CuAl and Cu filters. As a surrogate of image quality, the number of identifiable lung vessels was counted on a transversal micro-CT slice. Measured radiation doses varied from 0.09 Gy up to 5.18 Gy dependent on resolution and filter settings. A significant dose reduction of > 75% was achieved by a Cu filter when compared to an Al0.5 filter. However, this resulted in a markedly reduced image quality and interpretability of microstructures due to higher radiation shielding and lower spatial resolution. Thus, the right combination of distinct filters and several scan protocol settings adjusted to the individual requirements can significantly reduce the radiation dose of micro-CT leading to a higher animal welfare standard.