The quantitative measurement is required for fracture healing evaluation in clinical studies approaching toward Evidence Based Medicine. Early detection of fracture healing impairment is demanded to introduce as early as possible the optimal treatment leading to recovery. Clinically validated and tested methods usually utilize X-ray and CT data. The aim of this study was to improve assessment of fracture healing progress or impairment examined with X-ray and computed tomography (CT) and to determine the usefulness of quantitative methods based on newly developed 3D image analyzing software. An original software “3D Reconstructor” was developed. The application operates on medical image data stored in DICOM format. 3D Reconstructor v.2.0 allows 2D reconstruction in custom surface directs through data block and 3D reconstruction as well. The usefulness of the application was evaluated for long bone fracture healing with three-dimensional presentation of fracture callus. Twenty otherwise healthy fracture patients (average age 43 years) with fractures of the tibial shaft, humerus, forearm, and clavicle were enrolled and underwent chronological series X-ray imaging and spiral CT scanning when it was clinically justified and necessary. Patients were preselected for CT study because of healing impairment suspicion. Computer Tomography examination was performed 14 to 56 weeks after injury (GE Pro Speed SX, slice 2–3 mm, image reconstruction 1 – 1,5 mm, 120 kV, 100 mAs). Qualitative assessment included fracture line/margins, fracture gap, external callus appearance, callus-to-cortex ratio, bridging, and radiologic union. Quantitative assessment of CT density changes (Hounsfield units [HU]) in the fracture gap was performed in patients using 3D Reconstructor multimodality image analysis software. Regions of interest (ROI) were analyzed in details by quantitative and qualitative assessment. Complete bone union was confirmed in 2 cases, delayed union in 8 cases and nonunions in 10 cases. The use of 3D Reconstructor enhanced quantitative evaluation of fracture callus in all evaluated cases. Low union rate observed in computed tomography derives from patient’s preselection based on clinical observations. Reliable fracture healing assessment can be enhanced with computed tomography and Computer Aided Diagnostic methods that supplement quantitative analysis of CT images. CAD quantitative assessment of the fracture gap and callus was successfully performed using 3D Reconstructor software in clinical cases. Higher accuracy of pseudoarthrosis and delayed union diagnosis was achieved. The reliable diagnosis in fracture cases may be supported with Computer Aided Diagnostic Methods. Still ongoing project, “3D Reconstructor” seems to be more accurate over not “armed” evaluation of original CT DICOM files of fracture healing in selected cases.