Micro-CT is becoming a gold standard for quantitative imaging in preclinical disease models in bone research. Osteoporosis research routinely uses microCT for 3D analysis of the architecture and mechanical competence of trabecular and cortical bone. While most published methodological research on microCT in bone has focused on osteoporosis, there is equal potential for microCT to quantitatively assess other bone disease models (and genetic phenotypes). Here a unified analysis approach or “pipeline” is presented for all preclinical bone research models, consisting of a series of steps: (i) the scan and reconstruction; (ii) standardized 3D image orientation; (iii) anatomically referenced volume of interest (VOI) delineation; (iv) segmentation and 3D analysis, with (v) application-specific interpretation of measured parameters. How this pipeline works in practice is described for several applications beyond osteoporosis (covered elsewhere in this volume): arthritis bone effects, arthritis cartilage effects, bone tumor, and fracture callus healing. All these analyses can be performed in a single software environment and morphometry pipeline.