A　prototype　cone-beam　micro-CT　system　for　small　animal　imaging　has　been　developed　by　our　group　recently,　which　consists　of　a　microfocus　X-ray　source,　a　three-dimensional　programmable　stage　with　object　holder,　and　a　flat-panel　X-ray　detector.　It　has　a　large　field　of　view　(FOV),　which　can　acquire　the　whole　body　imaging　of　a　normal-size　mouse　in　a　single　scan　which　usually　takes　about　several　minutes　or　tens　of　minutes.　FDK　method　is　adopted　for　3D　reconstruction　with　Graphics　Processing　Unit　(GPU)　acceleration.　In　order　to　reconstruct　images　with　high　spatial　resolution　and　low　artifacts,　raw　data　preprocessing　and　geometry　calibration　are　implemented　before　reconstruction.　A　method　which　utilizes　a　wire　phantom　to　estimate　the　residual　horizontal　offset　of　the　detector　is　proposed,　and　1D　point　spread　function　is　used　to　assess　the　performance　of　geometric　calibration　quantitatively.　System　spatial　resolution,　image　uniformity　and　noise,　and　low　contrast　resolution　have　been　studied.　Mouse　images　with　and　without　contrast　agent　are　illuminated　in　this　paper.　Experimental　results　show　that　the　system　is　suitable　for　small　animal　imaging　and　is　adequate　to　provide　high-resolution　anatomic　information　for　bioluminescence　tomography　to　build　a　dual　modality　system.　©　2009　Shouping　Zhu　et　al.